# -*- encoding:utf-8 -*- from __future__ import division, absolute_import, print_function import re import sys import textwrap import warnings import jinja2 from numpydoc.docscrape import ( NumpyDocString, FunctionDoc, ClassDoc, ParseError ) from numpydoc.docscrape_sphinx import (SphinxDocString, SphinxClassDoc, SphinxFunctionDoc) from nose.tools import (assert_equal, assert_raises, assert_list_equal, assert_true) assert_list_equal.__self__.maxDiff = None 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 (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. no_description 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) doc_yields_txt = """ Test generator Yields ------ a : int The number of apples. b : int The number of bananas. int The number of unknowns. """ doc_yields = NumpyDocString(doc_yields_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][-1] == ' (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']), 3) 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.') arg, arg_type, desc = doc['Returns'][2] assert_equal(arg, 'no_description') assert_equal(arg_type, '') assert not ''.join(desc).strip() def test_yields(): section = doc_yields['Yields'] assert_equal(len(section), 3) truth = [('a', 'int', 'apples.'), ('b', 'int', 'bananas.'), ('int', '', 'unknowns.')] for (arg, arg_type, desc), (arg_, arg_type_, end) in zip(section, truth): assert_equal(arg, arg_) assert_equal(arg_type, arg_type_) assert desc[0].startswith('The number of') assert desc[0].endswith(end) def test_returnyield(): doc_text = """ Test having returns and yields. Returns ------- int The number of apples. Yields ------ a : int The number of apples. b : int The number of bananas. """ assert_raises(ValueError, NumpyDocString, doc_text) def test_section_twice(): doc_text = """ Test having a section Notes twice Notes ----- See the next note for more information Notes ----- That should break... """ assert_raises(ValueError, NumpyDocString, doc_text) # if we have a numpydoc object, we know where the error came from class Dummy(object): """ Dummy class. Notes ----- First note. Notes ----- Second note. """ def spam(self, a, b): """Spam\n\nSpam spam.""" pass def ham(self, c, d): """Cheese\n\nNo cheese.""" pass def dummy_func(arg): """ Dummy function. Notes ----- First note. Notes ----- Second note. """ try: SphinxClassDoc(Dummy) except ValueError as e: # python 3 version or python 2 version assert_true("test_section_twice..Dummy" in str(e) or 'test_docscrape.Dummy' in str(e)) try: SphinxFunctionDoc(dummy_func) except ValueError as e: # python 3 version or python 2 version assert_true("test_section_twice..dummy_func" in str(e) or 'function dummy_func' in str(e)) 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 _strip_blank_lines(s): "Remove leading, trailing and multiple blank lines" s = re.sub(r'^\s*\n', '', s) s = re.sub(r'\n\s*$', '', s) s = re.sub(r'\n\s*\n', r'\n\n', s) return s def line_by_line_compare(a, b): a = textwrap.dedent(a) b = textwrap.dedent(b) a = [l.rstrip() for l in _strip_blank_lines(a).split('\n')] b = [l.rstrip() for l in _strip_blank_lines(b).split('\n')] assert_list_equal(a, b) def test_str(): # doc_txt has the order of Notes and See Also sections flipped. # This should be handled automatically, and so, one thing this test does # is to make sure that See Also precedes Notes in the output. 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 (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. no_description 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_yield_str(): line_by_line_compare(str(doc_yields), """Test generator Yields ------ a : int The number of apples. b : int The number of bananas. int The number of unknowns. .. index:: """) def test_sphinx_str(): sphinx_doc = SphinxDocString(doc_txt) 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 (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. no_description .. :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] """) def test_sphinx_yields_str(): sphinx_doc = SphinxDocString(doc_yields_txt) line_by_line_compare(str(sphinx_doc), """Test generator :Yields: a : int The number of apples. b : int The number of bananas. int The number of unknowns. """) 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)') def my_func(a, b, **kwargs): pass fdoc = FunctionDoc(func=my_func) assert_equal(fdoc['Signature'], 'my_func(a, b, \*\*kwargs)') 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` :obj:`~baz.obj_r` :class:`class_j`: fubar foobar """) assert len(doc6['See Also']) == 13 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', '~baz.obj_r'): assert(not desc) else: assert(desc) if func == 'func_h': assert role == 'meth' elif func == 'baz.obj_q' or func == '~baz.obj_r': 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_parse_error(): text = ( """ z(x,theta) See Also -------- :func:`~foo` """) with assert_raises(ParseError) as err: NumpyDocString(text) assert_equal( str(r":func:`~foo` is not a item name in '\n z(x,theta)\n\n See Also\n --------\n :func:`~foo`\n '"), str(err.exception) ) 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) def test_unknown_section(): doc_text = """ Test having an unknown section Mope ---- This should be ignored and warned about """ class BadSection(object): """Class with bad section. Nope ---- This class has a nope section. """ pass with warnings.catch_warnings(record=True) as w: NumpyDocString(doc_text) assert len(w) == 1 assert "Unknown section Mope" == str(w[0].message) with warnings.catch_warnings(record=True) as w: SphinxClassDoc(BadSection) assert len(w) == 1 assert_true('test_docscrape.test_unknown_section..BadSection' in str(w[0].message) or 'test_docscrape.BadSection' in str(w[0].message)) 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 -------- >>> from matplotlib import 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_use_blockquotes(): cfg = dict(use_blockquotes=True) doc = SphinxDocString(""" Parameters ---------- abc : def ghi jkl mno Returns ------- ABC : DEF GHI JKL MNO """, config=cfg) line_by_line_compare(str(doc), ''' :Parameters: **abc** : def ghi **jkl** mno :Returns: **ABC** : DEF GHI **JKL** MNO ''') 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) class SubDummy(Dummy): """ Subclass of Dummy class. """ def ham(self, c, d): """Cheese\n\nNo cheese.\nOverloaded Dummy.ham""" pass def bar(self, a, b): """Bar\n\nNo bar""" pass for cls in (ClassDoc, SphinxClassDoc): doc = cls(SubDummy, config=dict(show_class_members=True, show_inherited_class_members=False)) assert 'Methods' in str(doc), (cls, str(doc)) assert 'spam' not in str(doc), (cls, str(doc)) assert 'ham' in str(doc), (cls, str(doc)) assert 'bar' in str(doc), (cls, str(doc)) assert 'spammity' not in str(doc), (cls, str(doc)) if cls is SphinxClassDoc: assert '.. autosummary::' in str(doc), str(doc) else: assert 'Spammity index' not in str(doc), str(doc) doc = cls(SubDummy, config=dict(show_class_members=True, show_inherited_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 'bar' 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. * hello * world an_attribute : float The docstring is printed instead no_docstring : str But a description no_docstring2 : str multiline_sentence midword_period no_period Methods ------- a b c Examples -------- For usage examples, see `ode`. """ def test_class_members_doc(): doc = ClassDoc(None, class_doc_txt) 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. * hello * world an_attribute : float The docstring is printed instead no_docstring : str But a description no_docstring2 : str multiline_sentence midword_period no_period Methods ------- a b c .. index:: """) def test_class_members_doc_sphinx(): class Foo: @property def an_attribute(self): """Test attribute""" return None @property def no_docstring(self): return None @property def no_docstring2(self): return None @property def multiline_sentence(self): """This is a sentence. It spans multiple lines.""" return None @property def midword_period(self): """The sentence for numpy.org.""" return None @property def no_period(self): """This does not have a period so we truncate its summary to the first linebreak Apparently. """ return None doc = SphinxClassDoc(Foo, class_doc_txt) 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`. :Attributes: t : float Current time. y : ndarray Current variable values. * hello * world :obj:`an_attribute ` : float Test attribute no_docstring : str But a description no_docstring2 : str .. :obj:`multiline_sentence ` This is a sentence. :obj:`midword_period ` The sentence for numpy.org. :obj:`no_period ` This does not have a period .. rubric:: Methods ===== ========== **a** **b** **c** ===== ========== """) def test_templated_sections(): doc = SphinxClassDoc(None, class_doc_txt, config={'template': jinja2.Template('{{examples}}\n{{parameters}}')}) line_by_line_compare(str(doc), """ .. rubric:: Examples For usage examples, see `ode`. :Parameters: f : callable ``f(t, y, *f_args)`` Aaa. jac : callable ``jac(t, y, *jac_args)`` Bbb. """) if __name__ == "__main__": import nose nose.run()