model of DCN pyramidal neuron
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# -*- encoding:utf-8 -*-
from __future__ import division, absolute_import, print_function
import sys, textwrap
from numpydoc.docscrape import NumpyDocString, FunctionDoc, ClassDoc
from numpydoc.docscrape_sphinx import SphinxDocString, SphinxClassDoc
from nose.tools import *
if sys.version_info[0] >= 3:
sixu = lambda s: s
else:
sixu = lambda s: unicode(s, "unicode_escape")
doc_txt = """\
numpy.multivariate_normal(mean, cov, shape=None, spam=None)
Draw values from a multivariate normal distribution with specified
mean and covariance.
The multivariate normal or Gaussian distribution is a generalisation
of the one-dimensional normal distribution to higher dimensions.
Parameters
----------
mean : (N,) ndarray
Mean of the N-dimensional distribution.
.. math::
(1+2+3)/3
cov : (N, N) ndarray
Covariance matrix of the distribution.
shape : tuple of ints
Given a shape of, for example, (m,n,k), m*n*k samples are
generated, and packed in an m-by-n-by-k arrangement. Because
each sample is N-dimensional, the output shape is (m,n,k,N).
Returns
-------
out : ndarray
The drawn samples, arranged according to `shape`. If the
shape given is (m,n,...), then the shape of `out` is is
(m,n,...,N).
In other words, each entry ``out[i,j,...,:]`` is an N-dimensional
value drawn from the distribution.
list of str
This is not a real return value. It exists to test
anonymous return values.
Other Parameters
----------------
spam : parrot
A parrot off its mortal coil.
Raises
------
RuntimeError
Some error
Warns
-----
RuntimeWarning
Some warning
Warnings
--------
Certain warnings apply.
Notes
-----
Instead of specifying the full covariance matrix, popular
approximations include:
- Spherical covariance (`cov` is a multiple of the identity matrix)
- Diagonal covariance (`cov` has non-negative elements only on the diagonal)
This geometrical property can be seen in two dimensions by plotting
generated data-points:
>>> mean = [0,0]
>>> cov = [[1,0],[0,100]] # diagonal covariance, points lie on x or y-axis
>>> x,y = multivariate_normal(mean,cov,5000).T
>>> plt.plot(x,y,'x'); plt.axis('equal'); plt.show()
Note that the covariance matrix must be symmetric and non-negative
definite.
References
----------
.. [1] A. Papoulis, "Probability, Random Variables, and Stochastic
Processes," 3rd ed., McGraw-Hill Companies, 1991
.. [2] R.O. Duda, P.E. Hart, and D.G. Stork, "Pattern Classification,"
2nd ed., Wiley, 2001.
See Also
--------
some, other, funcs
otherfunc : relationship
Examples
--------
>>> mean = (1,2)
>>> cov = [[1,0],[1,0]]
>>> x = multivariate_normal(mean,cov,(3,3))
>>> print x.shape
(3, 3, 2)
The following is probably true, given that 0.6 is roughly twice the
standard deviation:
>>> print list( (x[0,0,:] - mean) < 0.6 )
[True, True]
.. index:: random
:refguide: random;distributions, random;gauss
"""
doc = NumpyDocString(doc_txt)
def test_signature():
assert doc["Signature"].startswith("numpy.multivariate_normal(")
assert doc["Signature"].endswith("spam=None)")
def test_summary():
assert doc["Summary"][0].startswith("Draw values")
assert doc["Summary"][-1].endswith("covariance.")
def test_extended_summary():
assert doc["Extended Summary"][0].startswith("The multivariate normal")
def test_parameters():
assert_equal(len(doc["Parameters"]), 3)
assert_equal([n for n, _, _ in doc["Parameters"]], ["mean", "cov", "shape"])
arg, arg_type, desc = doc["Parameters"][1]
assert_equal(arg_type, "(N, N) ndarray")
assert desc[0].startswith("Covariance matrix")
assert doc["Parameters"][0][-1][-2] == " (1+2+3)/3"
def test_other_parameters():
assert_equal(len(doc["Other Parameters"]), 1)
assert_equal([n for n, _, _ in doc["Other Parameters"]], ["spam"])
arg, arg_type, desc = doc["Other Parameters"][0]
assert_equal(arg_type, "parrot")
assert desc[0].startswith("A parrot off its mortal coil")
def test_returns():
assert_equal(len(doc["Returns"]), 2)
arg, arg_type, desc = doc["Returns"][0]
assert_equal(arg, "out")
assert_equal(arg_type, "ndarray")
assert desc[0].startswith("The drawn samples")
assert desc[-1].endswith("distribution.")
arg, arg_type, desc = doc["Returns"][1]
assert_equal(arg, "list of str")
assert_equal(arg_type, "")
assert desc[0].startswith("This is not a real")
assert desc[-1].endswith("anonymous return values.")
def test_notes():
assert doc["Notes"][0].startswith("Instead")
assert doc["Notes"][-1].endswith("definite.")
assert_equal(len(doc["Notes"]), 17)
def test_references():
assert doc["References"][0].startswith("..")
assert doc["References"][-1].endswith("2001.")
def test_examples():
assert doc["Examples"][0].startswith(">>>")
assert doc["Examples"][-1].endswith("True]")
def test_index():
assert_equal(doc["index"]["default"], "random")
assert_equal(len(doc["index"]), 2)
assert_equal(len(doc["index"]["refguide"]), 2)
def non_blank_line_by_line_compare(a, b):
a = textwrap.dedent(a)
b = textwrap.dedent(b)
a = [l.rstrip() for l in a.split("\n") if l.strip()]
b = [l.rstrip() for l in b.split("\n") if l.strip()]
for n, line in enumerate(a):
if not line == b[n]:
raise AssertionError(
"Lines %s of a and b differ: " "\n>>> %s\n<<< %s\n" % (n, line, b[n])
)
def test_str():
non_blank_line_by_line_compare(
str(doc),
"""numpy.multivariate_normal(mean, cov, shape=None, spam=None)
Draw values from a multivariate normal distribution with specified
mean and covariance.
The multivariate normal or Gaussian distribution is a generalisation
of the one-dimensional normal distribution to higher dimensions.
Parameters
----------
mean : (N,) ndarray
Mean of the N-dimensional distribution.
.. math::
(1+2+3)/3
cov : (N, N) ndarray
Covariance matrix of the distribution.
shape : tuple of ints
Given a shape of, for example, (m,n,k), m*n*k samples are
generated, and packed in an m-by-n-by-k arrangement. Because
each sample is N-dimensional, the output shape is (m,n,k,N).
Returns
-------
out : ndarray
The drawn samples, arranged according to `shape`. If the
shape given is (m,n,...), then the shape of `out` is is
(m,n,...,N).
In other words, each entry ``out[i,j,...,:]`` is an N-dimensional
value drawn from the distribution.
list of str
This is not a real return value. It exists to test
anonymous return values.
Other Parameters
----------------
spam : parrot
A parrot off its mortal coil.
Raises
------
RuntimeError
Some error
Warns
-----
RuntimeWarning
Some warning
Warnings
--------
Certain warnings apply.
See Also
--------
`some`_, `other`_, `funcs`_
`otherfunc`_
relationship
Notes
-----
Instead of specifying the full covariance matrix, popular
approximations include:
- Spherical covariance (`cov` is a multiple of the identity matrix)
- Diagonal covariance (`cov` has non-negative elements only on the diagonal)
This geometrical property can be seen in two dimensions by plotting
generated data-points:
>>> mean = [0,0]
>>> cov = [[1,0],[0,100]] # diagonal covariance, points lie on x or y-axis
>>> x,y = multivariate_normal(mean,cov,5000).T
>>> plt.plot(x,y,'x'); plt.axis('equal'); plt.show()
Note that the covariance matrix must be symmetric and non-negative
definite.
References
----------
.. [1] A. Papoulis, "Probability, Random Variables, and Stochastic
Processes," 3rd ed., McGraw-Hill Companies, 1991
.. [2] R.O. Duda, P.E. Hart, and D.G. Stork, "Pattern Classification,"
2nd ed., Wiley, 2001.
Examples
--------
>>> mean = (1,2)
>>> cov = [[1,0],[1,0]]
>>> x = multivariate_normal(mean,cov,(3,3))
>>> print x.shape
(3, 3, 2)
The following is probably true, given that 0.6 is roughly twice the
standard deviation:
>>> print list( (x[0,0,:] - mean) < 0.6 )
[True, True]
.. index:: random
:refguide: random;distributions, random;gauss""",
)
def test_sphinx_str():
sphinx_doc = SphinxDocString(doc_txt)
non_blank_line_by_line_compare(
str(sphinx_doc),
"""
.. index:: random
single: random;distributions, random;gauss
Draw values from a multivariate normal distribution with specified
mean and covariance.
The multivariate normal or Gaussian distribution is a generalisation
of the one-dimensional normal distribution to higher dimensions.
:Parameters:
**mean** : (N,) ndarray
Mean of the N-dimensional distribution.
.. math::
(1+2+3)/3
**cov** : (N, N) ndarray
Covariance matrix of the distribution.
**shape** : tuple of ints
Given a shape of, for example, (m,n,k), m*n*k samples are
generated, and packed in an m-by-n-by-k arrangement. Because
each sample is N-dimensional, the output shape is (m,n,k,N).
:Returns:
**out** : ndarray
The drawn samples, arranged according to `shape`. If the
shape given is (m,n,...), then the shape of `out` is is
(m,n,...,N).
In other words, each entry ``out[i,j,...,:]`` is an N-dimensional
value drawn from the distribution.
list of str
This is not a real return value. It exists to test
anonymous return values.
:Other Parameters:
**spam** : parrot
A parrot off its mortal coil.
:Raises:
**RuntimeError**
Some error
:Warns:
**RuntimeWarning**
Some warning
.. warning::
Certain warnings apply.
.. seealso::
:obj:`some`, :obj:`other`, :obj:`funcs`
:obj:`otherfunc`
relationship
.. rubric:: Notes
Instead of specifying the full covariance matrix, popular
approximations include:
- Spherical covariance (`cov` is a multiple of the identity matrix)
- Diagonal covariance (`cov` has non-negative elements only on the diagonal)
This geometrical property can be seen in two dimensions by plotting
generated data-points:
>>> mean = [0,0]
>>> cov = [[1,0],[0,100]] # diagonal covariance, points lie on x or y-axis
>>> x,y = multivariate_normal(mean,cov,5000).T
>>> plt.plot(x,y,'x'); plt.axis('equal'); plt.show()
Note that the covariance matrix must be symmetric and non-negative
definite.
.. rubric:: References
.. [1] A. Papoulis, "Probability, Random Variables, and Stochastic
Processes," 3rd ed., McGraw-Hill Companies, 1991
.. [2] R.O. Duda, P.E. Hart, and D.G. Stork, "Pattern Classification,"
2nd ed., Wiley, 2001.
.. only:: latex
[1]_, [2]_
.. rubric:: Examples
>>> mean = (1,2)
>>> cov = [[1,0],[1,0]]
>>> x = multivariate_normal(mean,cov,(3,3))
>>> print x.shape
(3, 3, 2)
The following is probably true, given that 0.6 is roughly twice the
standard deviation:
>>> print list( (x[0,0,:] - mean) < 0.6 )
[True, True]
""",
)
doc2 = NumpyDocString(
"""
Returns array of indices of the maximum values of along the given axis.
Parameters
----------
a : {array_like}
Array to look in.
axis : {None, integer}
If None, the index is into the flattened array, otherwise along
the specified axis"""
)
def test_parameters_without_extended_description():
assert_equal(len(doc2["Parameters"]), 2)
doc3 = NumpyDocString(
"""
my_signature(*params, **kwds)
Return this and that.
"""
)
def test_escape_stars():
signature = str(doc3).split("\n")[0]
assert_equal(signature, "my_signature(\*params, \*\*kwds)")
doc4 = NumpyDocString(
"""a.conj()
Return an array with all complex-valued elements conjugated."""
)
def test_empty_extended_summary():
assert_equal(doc4["Extended Summary"], [])
doc5 = NumpyDocString(
"""
a.something()
Raises
------
LinAlgException
If array is singular.
Warns
-----
SomeWarning
If needed
"""
)
def test_raises():
assert_equal(len(doc5["Raises"]), 1)
name, _, desc = doc5["Raises"][0]
assert_equal(name, "LinAlgException")
assert_equal(desc, ["If array is singular."])
def test_warns():
assert_equal(len(doc5["Warns"]), 1)
name, _, desc = doc5["Warns"][0]
assert_equal(name, "SomeWarning")
assert_equal(desc, ["If needed"])
def test_see_also():
doc6 = NumpyDocString(
"""
z(x,theta)
See Also
--------
func_a, func_b, func_c
func_d : some equivalent func
foo.func_e : some other func over
multiple lines
func_f, func_g, :meth:`func_h`, func_j,
func_k
:obj:`baz.obj_q`
:class:`class_j`: fubar
foobar
"""
)
assert len(doc6["See Also"]) == 12
for func, desc, role in doc6["See Also"]:
if func in (
"func_a",
"func_b",
"func_c",
"func_f",
"func_g",
"func_h",
"func_j",
"func_k",
"baz.obj_q",
):
assert not desc
else:
assert desc
if func == "func_h":
assert role == "meth"
elif func == "baz.obj_q":
assert role == "obj"
elif func == "class_j":
assert role == "class"
else:
assert role is None
if func == "func_d":
assert desc == ["some equivalent func"]
elif func == "foo.func_e":
assert desc == ["some other func over", "multiple lines"]
elif func == "class_j":
assert desc == ["fubar", "foobar"]
def test_see_also_print():
class Dummy(object):
"""
See Also
--------
func_a, func_b
func_c : some relationship
goes here
func_d
"""
pass
obj = Dummy()
s = str(FunctionDoc(obj, role="func"))
assert ":func:`func_a`, :func:`func_b`" in s
assert " some relationship" in s
assert ":func:`func_d`" in s
doc7 = NumpyDocString(
"""
Doc starts on second line.
"""
)
def test_empty_first_line():
assert doc7["Summary"][0].startswith("Doc starts")
def test_no_summary():
str(
SphinxDocString(
"""
Parameters
----------"""
)
)
def test_unicode():
doc = SphinxDocString(
"""
öäöäöäöäöåååå
öäöäöäööäååå
Parameters
----------
ååå : äää
ööö
Returns
-------
ååå : ööö
äää
"""
)
assert isinstance(doc["Summary"][0], str)
assert doc["Summary"][0] == "öäöäöäöäöåååå"
def test_plot_examples():
cfg = dict(use_plots=True)
doc = SphinxDocString(
"""
Examples
--------
>>> import matplotlib.pyplot as plt
>>> plt.plot([1,2,3],[4,5,6])
>>> plt.show()
""",
config=cfg,
)
assert "plot::" in str(doc), str(doc)
doc = SphinxDocString(
"""
Examples
--------
.. plot::
import matplotlib.pyplot as plt
plt.plot([1,2,3],[4,5,6])
plt.show()
""",
config=cfg,
)
assert str(doc).count("plot::") == 1, str(doc)
def test_class_members():
class Dummy(object):
"""
Dummy class.
"""
def spam(self, a, b):
"""Spam\n\nSpam spam."""
pass
def ham(self, c, d):
"""Cheese\n\nNo cheese."""
pass
@property
def spammity(self):
"""Spammity index"""
return 0.95
class Ignorable(object):
"""local class, to be ignored"""
pass
for cls in (ClassDoc, SphinxClassDoc):
doc = cls(Dummy, config=dict(show_class_members=False))
assert "Methods" not in str(doc), (cls, str(doc))
assert "spam" not in str(doc), (cls, str(doc))
assert "ham" not in str(doc), (cls, str(doc))
assert "spammity" not in str(doc), (cls, str(doc))
assert "Spammity index" not in str(doc), (cls, str(doc))
doc = cls(Dummy, config=dict(show_class_members=True))
assert "Methods" in str(doc), (cls, str(doc))
assert "spam" in str(doc), (cls, str(doc))
assert "ham" in str(doc), (cls, str(doc))
assert "spammity" in str(doc), (cls, str(doc))
if cls is SphinxClassDoc:
assert ".. autosummary::" in str(doc), str(doc)
else:
assert "Spammity index" in str(doc), str(doc)
def test_duplicate_signature():
# Duplicate function signatures occur e.g. in ufuncs, when the
# automatic mechanism adds one, and a more detailed comes from the
# docstring itself.
doc = NumpyDocString(
"""
z(x1, x2)
z(a, theta)
"""
)
assert doc["Signature"].strip() == "z(a, theta)"
class_doc_txt = """
Foo
Parameters
----------
f : callable ``f(t, y, *f_args)``
Aaa.
jac : callable ``jac(t, y, *jac_args)``
Bbb.
Attributes
----------
t : float
Current time.
y : ndarray
Current variable values.
Methods
-------
a
b
c
Examples
--------
For usage examples, see `ode`.
"""
def test_class_members_doc():
doc = ClassDoc(None, class_doc_txt)
non_blank_line_by_line_compare(
str(doc),
"""
Foo
Parameters
----------
f : callable ``f(t, y, *f_args)``
Aaa.
jac : callable ``jac(t, y, *jac_args)``
Bbb.
Examples
--------
For usage examples, see `ode`.
Attributes
----------
t : float
Current time.
y : ndarray
Current variable values.
Methods
-------
a
b
c
.. index::
""",
)
def test_class_members_doc_sphinx():
doc = SphinxClassDoc(None, class_doc_txt)
non_blank_line_by_line_compare(
str(doc),
"""
Foo
:Parameters:
**f** : callable ``f(t, y, *f_args)``
Aaa.
**jac** : callable ``jac(t, y, *jac_args)``
Bbb.
.. rubric:: Examples
For usage examples, see `ode`.
.. rubric:: Attributes
=== ==========
t (float) Current time.
y (ndarray) Current variable values.
=== ==========
.. rubric:: Methods
=== ==========
a
b
c
=== ==========
""",
)
if __name__ == "__main__":
import nose
nose.run()