Merge pull request dipy#3342 from deka27/doctest-warnings

RF: Doctest warnings

dipy/core/geometry.py

@@ -610,17 +610,17 @@ def euler_matrix(ai, aj, ak, *, axes="sxyz"):
     Examples
     --------
     >>> import numpy
-    >>> R = euler_matrix(1, 2, 3, 'syxz')
+    >>> R = euler_matrix(1, 2, 3, axes='syxz')
     >>> numpy.allclose(numpy.sum(R[0]), -1.34786452)
     True
-    >>> R = euler_matrix(1, 2, 3, (0, 1, 0, 1))
+    >>> R = euler_matrix(1, 2, 3, axes=(0, 1, 0, 1))
     >>> numpy.allclose(numpy.sum(R[0]), -0.383436184)
     True
     >>> ai, aj, ak = (4.0*math.pi) * (numpy.random.random(3) - 0.5)
     >>> for axes in _AXES2TUPLE.keys():
-    ...    _ = euler_matrix(ai, aj, ak, axes)
+    ...    _ = euler_matrix(ai, aj, ak, axes=axes)
     >>> for axes in _TUPLE2AXES.keys():
-    ...    _ = euler_matrix(ai, aj, ak, axes)
+    ...    _ = euler_matrix(ai, aj, ak, axes=axes)
 
     """
     try:
@@ -706,7 +706,9 @@ def compose_matrix(
     >>> angles = (np.random.random(3) - 0.5) * (2*math.pi)
     >>> trans = np.random.random(3) - 0.5
     >>> persp = np.random.random(4) - 0.5
-    >>> M0 = gm.compose_matrix(scale, shear, angles, trans, persp)
+    >>> M0 = gm.compose_matrix(
+    ...     scale=scale, shear=shear, angles=angles, translate=trans, perspective=persp
+    ... )
 
     """
     M = np.identity(4)

dipy/core/graph.py

@@ -20,10 +20,10 @@ def __init__(self):
         --------
         >>> from dipy.core.graph import Graph
         >>> g=Graph()
-        >>> g.add_node('a',5)
-        >>> g.add_node('b',6)
-        >>> g.add_node('c',10)
-        >>> g.add_node('d',11)
+        >>> g.add_node('a', attr=5)
+        >>> g.add_node('b', attr=6)
+        >>> g.add_node('c', attr=10)
+        >>> g.add_node('d', attr=11)
         >>> g.add_edge('a','b')
         >>> g.add_edge('b','c')
         >>> g.add_edge('c','d')

dipy/core/sphere_stats.py

@@ -39,10 +39,10 @@ def random_uniform_on_sphere(*, n=1, coords="xyz"):
     Examples
     --------
     >>> from dipy.core.sphere_stats import random_uniform_on_sphere
-    >>> X = random_uniform_on_sphere(4, 'radians')
+    >>> X = random_uniform_on_sphere(n=4, coords='radians')
     >>> X.shape == (4, 2)
     True
-    >>> X = random_uniform_on_sphere(4, 'xyz')
+    >>> X = random_uniform_on_sphere(n=4, coords='xyz')
     >>> X.shape == (4, 3)
     True
     """

dipy/data/__init__.py

@@ -171,7 +171,7 @@ def get_sim_voxels(*, name="fib1"):
     Examples
     --------
     >>> from dipy.data import get_sim_voxels
-    >>> sv=get_sim_voxels('fib1')
+    >>> sv=get_sim_voxels(name='fib1')
     >>> sv['data'].shape == (100, 102)
     True
     >>> sv['fibres']
@@ -182,7 +182,7 @@ def get_sim_voxels(*, name="fib1"):
     True
     >>> sv['snr']
     '60'
-    >>> sv2=get_sim_voxels('fib2')
+    >>> sv2=get_sim_voxels(name='fib2')
     >>> sv2['fibres']
     '2'
     >>> sv2['snr']
@@ -217,7 +217,7 @@ def get_skeleton(*, name="C1"):
     Examples
     --------
     >>> from dipy.data import get_skeleton
-    >>> C=get_skeleton('C1')
+    >>> C=get_skeleton(name='C1')
     >>> len(C.keys())
     117
     >>> for c in C: break

dipy/io/dpy.py

@@ -41,15 +41,15 @@ def __init__(self, fname, *, mode="r", compression=0):
         >>> def dpy_example():
         ...     fd,fname = mkstemp()
         ...     fname += '.dpy'#add correct extension
-        ...     dpw = Dpy(fname,'w')
+        ...     dpw = Dpy(fname, mode='w')
         ...     A=np.ones((5,3))
         ...     B=2*A.copy()
         ...     C=3*A.copy()
         ...     dpw.write_track(A)
         ...     dpw.write_track(B)
         ...     dpw.write_track(C)
         ...     dpw.close()
-        ...     dpr = Dpy(fname,'r')
+        ...     dpr = Dpy(fname, mode='r')
         ...     dpr.read_track()
         ...     dpr.read_track()
         ...     dpr.read_tracksi([0, 1, 2, 0, 0, 2])

dipy/reconst/gqi.py

@@ -53,7 +53,7 @@ def __init__(self, gtab, method="gqi2", sampling_length=1.2, normalize_peaks=Fal
         >>> from dipy.data import dsi_voxels
         >>> data, gtab = dsi_voxels()
         >>> from dipy.core.subdivide_octahedron import create_unit_sphere
-        >>> sphere = create_unit_sphere(5)
+        >>> sphere = create_unit_sphere(recursion_level=5)
         >>> from dipy.reconst.gqi import GeneralizedQSamplingModel
         >>> gq = GeneralizedQSamplingModel(gtab, 'gqi2', 1.1)
         >>> voxel_signal = data[0, 0, 0]

dipy/stats/qc.py

@@ -30,7 +30,7 @@ def find_qspace_neighbors(gtab):
     >>> import numpy as np
     >>> gtab = gradient_table(
     ...     np.array([0, 1000, 1000, 2000]),
-    ...     np.array([
+    ...     bvecs=np.array([
     ...         [1, 0, 0],
     ...         [1, 0, 0],
     ...         [0.99, 0.0001, 0.0001],

dipy/tracking/metrics.py

@@ -302,15 +302,15 @@ def frenet_serret(xyz):
     dxyz = np.gradient(xyz)[0]
     ddxyz = np.gradient(dxyz)[0]
     # Tangent
-    T = np.divide(dxyz, magn(dxyz, 3))
+    T = np.divide(dxyz, magn(dxyz, n=3))
     # Derivative of Tangent
     dT = np.gradient(T)[0]
     # Normal
-    N = np.divide(dT, magn(dT, 3))
+    N = np.divide(dT, magn(dT, n=3))
     # Binormal
     B = np.cross(T, N)
     # Curvature
-    k = magn(np.cross(dxyz, ddxyz), 1) / (magn(dxyz, 1) ** 3)
+    k = magn(np.cross(dxyz, ddxyz), n=1) / (magn(dxyz, n=1) ** 3)
     # Torsion
     # (In matlab was t=dot(-B,N,2))
     t = np.sum(-B * N, axis=1)
@@ -358,7 +358,7 @@ def mean_curvature(xyz):
     ddxyz = np.gradient(dxyz)[0]
 
     # Curvature
-    k = magn(np.cross(dxyz, ddxyz), 1) / (magn(dxyz, 1) ** 3)
+    k = magn(np.cross(dxyz, ddxyz), n=1) / (magn(dxyz, n=1) ** 3)
 
     return np.mean(k)
 
@@ -452,7 +452,7 @@ def longest_track_bundle(bundle, *, sort=False):
     >>> longest_track_bundle(bundle)
     array([[0, 0, 0],
            [4, 4, 4]])
-    >>> longest_track_bundle(bundle, True) #doctest: +ELLIPSIS
+    >>> longest_track_bundle(bundle, sort=True) #doctest: +ELLIPSIS
     array([0, 1]...)
 
     """
@@ -665,7 +665,7 @@ def spline(xyz, *, s=3, k=2, nest=-1):
     >>> y+= np.random.normal(scale=0.1, size=y.shape)
     >>> z+= np.random.normal(scale=0.1, size=z.shape)
     >>> xyz=np.vstack((x,y,z)).T
-    >>> xyzn=spline(xyz,3,2,-1)
+    >>> xyzn=spline(xyz,s=3,k=2,nest=-1)
     >>> len(xyzn) > len(xyz)
     True
 

dipy/tracking/utils.py

@@ -380,7 +380,7 @@ def seeds_from_mask(mask, affine, *, density=(1, 1, 1)):
     --------
     >>> mask = np.zeros((3,3,3), 'bool')
     >>> mask[0,0,0] = 1
-    >>> seeds_from_mask(mask, np.eye(4), [1,1,1])
+    >>> seeds_from_mask(mask, np.eye(4), density=[1,1,1])
     array([[ 0.,  0.,  0.]])
 
     """

dipy/utils/deprecator.py

@@ -105,9 +105,9 @@ def cmp_pkg_version(version_str, *, pkg_version_str=__version__):
 
     Examples
     --------
-    >>> cmp_pkg_version('1.2.1', '1.2.0')
+    >>> cmp_pkg_version('1.2.1', pkg_version_str='1.2.0')
     1
-    >>> cmp_pkg_version('1.2.0dev', '1.2.0')
+    >>> cmp_pkg_version('1.2.0dev', pkg_version_str='1.2.0')
     -1
 
     """
@@ -277,7 +277,7 @@ def deprecated_params(
     The deprecation warnings are not shown in the following examples.
     To deprecate a positional or keyword argument::
     >>> from dipy.utils.deprecator import deprecated_params
-    >>> @deprecated_params('sig', 'sigma', '0.3')
+    >>> @deprecated_params('sig', new_name='sigma', since='0.3')
     ... def test(sigma):
     ...     return sigma
     >>> test(2)
@@ -290,8 +290,8 @@ def deprecated_params(
     It is also possible to replace multiple arguments. The ``old_name``,
     ``new_name`` and ``since`` have to be `tuple` or `list` and contain the
     same number of entries::
-    >>> @deprecated_params(['a', 'b'], ['alpha', 'beta'],
-    ...                    ['0.2', 0.4])
+    >>> @deprecated_params(['a', 'b'], new_name=['alpha', 'beta'],
+    ...                    since=['0.2', 0.4])
     ... def test(alpha, beta):
     ...     return alpha, beta
     >>> test(a=2, b=3)  # doctest: +SKIP