# -*- 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()