Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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444 lines
16 KiB
444 lines
16 KiB
"""
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tl;dr: all code code is licensed under simplified BSD, unless stated otherwise.
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Unless stated otherwise in the source files, all code is copyright 2010 David
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Wolever <david@wolever.net>. All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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THIS SOFTWARE IS PROVIDED BY <COPYRIGHT HOLDER> ``AS IS'' AND ANY EXPRESS OR
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IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
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MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
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EVENT SHALL <COPYRIGHT HOLDER> OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
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OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
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ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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The views and conclusions contained in the software and documentation are those
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of the authors and should not be interpreted as representing official policies,
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either expressed or implied, of David Wolever.
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"""
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import re
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import inspect
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import warnings
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from functools import wraps
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from types import MethodType
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from collections import namedtuple
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try:
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from collections import OrderedDict as MaybeOrderedDict
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except ImportError:
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MaybeOrderedDict = dict
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from unittest import TestCase
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_param = namedtuple("param", "args kwargs")
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class param(_param):
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""" Represents a single parameter to a test case.
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For example::
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>>> p = param("foo", bar=16)
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>>> p
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param("foo", bar=16)
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>>> p.args
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('foo', )
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>>> p.kwargs
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{'bar': 16}
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Intended to be used as an argument to ``@parameterized``::
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@parameterized([
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param("foo", bar=16),
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])
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def test_stuff(foo, bar=16):
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pass
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"""
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def __new__(cls, *args , **kwargs):
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return _param.__new__(cls, args, kwargs)
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@classmethod
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def explicit(cls, args=None, kwargs=None):
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""" Creates a ``param`` by explicitly specifying ``args`` and
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``kwargs``::
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>>> param.explicit([1,2,3])
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param(*(1, 2, 3))
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>>> param.explicit(kwargs={"foo": 42})
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param(*(), **{"foo": "42"})
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"""
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args = args or ()
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kwargs = kwargs or {}
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return cls(*args, **kwargs)
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@classmethod
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def from_decorator(cls, args):
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""" Returns an instance of ``param()`` for ``@parameterized`` argument
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``args``::
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>>> param.from_decorator((42, ))
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param(args=(42, ), kwargs={})
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>>> param.from_decorator("foo")
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param(args=("foo", ), kwargs={})
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"""
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if isinstance(args, param):
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return args
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elif isinstance(args, (str,)):
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args = (args, )
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try:
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return cls(*args)
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except TypeError as e:
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if "after * must be" not in str(e):
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raise
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raise TypeError(
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"Parameters must be tuples, but %r is not (hint: use '(%r, )')"
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%(args, args),
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)
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def __repr__(self):
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return "param(*%r, **%r)" %self
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class QuietOrderedDict(MaybeOrderedDict):
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""" When OrderedDict is available, use it to make sure that the kwargs in
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doc strings are consistently ordered. """
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__str__ = dict.__str__
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__repr__ = dict.__repr__
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def parameterized_argument_value_pairs(func, p):
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"""Return tuples of parameterized arguments and their values.
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This is useful if you are writing your own doc_func
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function and need to know the values for each parameter name::
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>>> def func(a, foo=None, bar=42, **kwargs): pass
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>>> p = param(1, foo=7, extra=99)
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>>> parameterized_argument_value_pairs(func, p)
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[("a", 1), ("foo", 7), ("bar", 42), ("**kwargs", {"extra": 99})]
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If the function's first argument is named ``self`` then it will be
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ignored::
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>>> def func(self, a): pass
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>>> p = param(1)
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>>> parameterized_argument_value_pairs(func, p)
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[("a", 1)]
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Additionally, empty ``*args`` or ``**kwargs`` will be ignored::
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>>> def func(foo, *args): pass
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>>> p = param(1)
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>>> parameterized_argument_value_pairs(func, p)
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[("foo", 1)]
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>>> p = param(1, 16)
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>>> parameterized_argument_value_pairs(func, p)
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[("foo", 1), ("*args", (16, ))]
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"""
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argspec = inspect.getargspec(func)
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arg_offset = 1 if argspec.args[:1] == ["self"] else 0
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named_args = argspec.args[arg_offset:]
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result = list(zip(named_args, p.args))
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named_args = argspec.args[len(result) + arg_offset:]
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varargs = p.args[len(result):]
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result.extend([
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(name, p.kwargs.get(name, default))
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for (name, default)
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in zip(named_args, argspec.defaults or [])
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])
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seen_arg_names = {n for (n, _) in result}
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keywords = QuietOrderedDict(sorted([
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(name, p.kwargs[name])
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for name in p.kwargs
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if name not in seen_arg_names
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]))
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if varargs:
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result.append(("*%s" %(argspec.varargs, ), tuple(varargs)))
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if keywords:
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result.append(("**%s" %(argspec.keywords, ), keywords))
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return result
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def short_repr(x, n=64):
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""" A shortened repr of ``x`` which is guaranteed to be ``unicode``::
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>>> short_repr("foo")
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u"foo"
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>>> short_repr("123456789", n=4)
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u"12...89"
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"""
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x_repr = repr(x)
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if isinstance(x_repr, bytes):
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try:
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x_repr = str(x_repr, "utf-8")
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except UnicodeDecodeError:
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x_repr = str(x_repr, "latin1")
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if len(x_repr) > n:
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x_repr = x_repr[:n//2] + "..." + x_repr[len(x_repr) - n//2:]
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return x_repr
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def default_doc_func(func, num, p):
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if func.__doc__ is None:
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return None
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all_args_with_values = parameterized_argument_value_pairs(func, p)
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# Assumes that the function passed is a bound method.
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descs = ["%s=%s" %(n, short_repr(v)) for n, v in all_args_with_values]
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# The documentation might be a multiline string, so split it
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# and just work with the first string, ignoring the period
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# at the end if there is one.
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first, nl, rest = func.__doc__.lstrip().partition("\n")
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suffix = ""
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if first.endswith("."):
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suffix = "."
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first = first[:-1]
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args = "%s[with %s]" %(len(first) and " " or "", ", ".join(descs))
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return "".join([first.rstrip(), args, suffix, nl, rest])
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def default_name_func(func, num, p):
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base_name = func.__name__
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name_suffix = "_%s" %(num, )
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if len(p.args) > 0 and isinstance(p.args[0], (str,)):
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name_suffix += "_" + parameterized.to_safe_name(p.args[0])
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return base_name + name_suffix
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# force nose for numpy purposes.
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_test_runner_override = 'nose'
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_test_runner_guess = False
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_test_runners = set(["unittest", "unittest2", "nose", "nose2", "pytest"])
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_test_runner_aliases = {
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"_pytest": "pytest",
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}
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def set_test_runner(name):
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global _test_runner_override
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if name not in _test_runners:
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raise TypeError(
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"Invalid test runner: %r (must be one of: %s)"
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%(name, ", ".join(_test_runners)),
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)
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_test_runner_override = name
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def detect_runner():
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""" Guess which test runner we're using by traversing the stack and looking
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for the first matching module. This *should* be reasonably safe, as
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it's done during test discovery where the test runner should be the
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stack frame immediately outside. """
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if _test_runner_override is not None:
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return _test_runner_override
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global _test_runner_guess
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if _test_runner_guess is False:
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stack = inspect.stack()
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for record in reversed(stack):
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frame = record[0]
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module = frame.f_globals.get("__name__").partition(".")[0]
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if module in _test_runner_aliases:
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module = _test_runner_aliases[module]
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if module in _test_runners:
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_test_runner_guess = module
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break
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else:
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_test_runner_guess = None
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return _test_runner_guess
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class parameterized:
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""" Parameterize a test case::
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class TestInt:
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@parameterized([
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("A", 10),
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("F", 15),
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param("10", 42, base=42)
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])
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def test_int(self, input, expected, base=16):
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actual = int(input, base=base)
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assert_equal(actual, expected)
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@parameterized([
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(2, 3, 5)
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(3, 5, 8),
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])
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def test_add(a, b, expected):
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assert_equal(a + b, expected)
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"""
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def __init__(self, input, doc_func=None):
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self.get_input = self.input_as_callable(input)
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self.doc_func = doc_func or default_doc_func
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def __call__(self, test_func):
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self.assert_not_in_testcase_subclass()
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@wraps(test_func)
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def wrapper(test_self=None):
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test_cls = test_self and type(test_self)
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original_doc = wrapper.__doc__
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for num, args in enumerate(wrapper.parameterized_input):
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p = param.from_decorator(args)
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unbound_func, nose_tuple = self.param_as_nose_tuple(test_self, test_func, num, p)
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try:
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wrapper.__doc__ = nose_tuple[0].__doc__
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# Nose uses `getattr(instance, test_func.__name__)` to get
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# a method bound to the test instance (as opposed to a
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# method bound to the instance of the class created when
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# tests were being enumerated). Set a value here to make
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# sure nose can get the correct test method.
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if test_self is not None:
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setattr(test_cls, test_func.__name__, unbound_func)
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yield nose_tuple
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finally:
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if test_self is not None:
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delattr(test_cls, test_func.__name__)
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wrapper.__doc__ = original_doc
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wrapper.parameterized_input = self.get_input()
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wrapper.parameterized_func = test_func
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test_func.__name__ = "_parameterized_original_%s" %(test_func.__name__, )
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return wrapper
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def param_as_nose_tuple(self, test_self, func, num, p):
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nose_func = wraps(func)(lambda *args: func(*args[:-1], **args[-1]))
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nose_func.__doc__ = self.doc_func(func, num, p)
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# Track the unbound function because we need to setattr the unbound
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# function onto the class for nose to work (see comments above), and
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# Python 3 doesn't let us pull the function out of a bound method.
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unbound_func = nose_func
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if test_self is not None:
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nose_func = MethodType(nose_func, test_self)
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return unbound_func, (nose_func, ) + p.args + (p.kwargs or {}, )
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def assert_not_in_testcase_subclass(self):
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parent_classes = self._terrible_magic_get_defining_classes()
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if any(issubclass(cls, TestCase) for cls in parent_classes):
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raise Exception("Warning: '@parameterized' tests won't work "
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"inside subclasses of 'TestCase' - use "
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"'@parameterized.expand' instead.")
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def _terrible_magic_get_defining_classes(self):
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""" Returns the set of parent classes of the class currently being defined.
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Will likely only work if called from the ``parameterized`` decorator.
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This function is entirely @brandon_rhodes's fault, as he suggested
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the implementation: http://stackoverflow.com/a/8793684/71522
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"""
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stack = inspect.stack()
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if len(stack) <= 4:
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return []
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frame = stack[4]
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code_context = frame[4] and frame[4][0].strip()
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if not (code_context and code_context.startswith("class ")):
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return []
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_, _, parents = code_context.partition("(")
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parents, _, _ = parents.partition(")")
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return eval("[" + parents + "]", frame[0].f_globals, frame[0].f_locals)
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@classmethod
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def input_as_callable(cls, input):
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if callable(input):
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return lambda: cls.check_input_values(input())
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input_values = cls.check_input_values(input)
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return lambda: input_values
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@classmethod
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def check_input_values(cls, input_values):
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# Explicitly convert non-list inputs to a list so that:
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# 1. A helpful exception will be raised if they aren't iterable, and
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# 2. Generators are unwrapped exactly once (otherwise `nosetests
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# --processes=n` has issues; see:
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# https://github.com/wolever/nose-parameterized/pull/31)
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if not isinstance(input_values, list):
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input_values = list(input_values)
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return [ param.from_decorator(p) for p in input_values ]
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@classmethod
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def expand(cls, input, name_func=None, doc_func=None, **legacy):
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""" A "brute force" method of parameterizing test cases. Creates new
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test cases and injects them into the namespace that the wrapped
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function is being defined in. Useful for parameterizing tests in
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subclasses of 'UnitTest', where Nose test generators don't work.
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>>> @parameterized.expand([("foo", 1, 2)])
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... def test_add1(name, input, expected):
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... actual = add1(input)
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... assert_equal(actual, expected)
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...
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>>> locals()
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... 'test_add1_foo_0': <function ...> ...
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>>>
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"""
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if "testcase_func_name" in legacy:
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warnings.warn("testcase_func_name= is deprecated; use name_func=",
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DeprecationWarning, stacklevel=2)
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if not name_func:
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name_func = legacy["testcase_func_name"]
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if "testcase_func_doc" in legacy:
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warnings.warn("testcase_func_doc= is deprecated; use doc_func=",
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DeprecationWarning, stacklevel=2)
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if not doc_func:
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doc_func = legacy["testcase_func_doc"]
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doc_func = doc_func or default_doc_func
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name_func = name_func or default_name_func
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def parameterized_expand_wrapper(f, instance=None):
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stack = inspect.stack()
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frame = stack[1]
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frame_locals = frame[0].f_locals
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parameters = cls.input_as_callable(input)()
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for num, p in enumerate(parameters):
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name = name_func(f, num, p)
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frame_locals[name] = cls.param_as_standalone_func(p, f, name)
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frame_locals[name].__doc__ = doc_func(f, num, p)
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f.__test__ = False
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return parameterized_expand_wrapper
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@classmethod
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def param_as_standalone_func(cls, p, func, name):
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@wraps(func)
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def standalone_func(*a):
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return func(*(a + p.args), **p.kwargs)
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standalone_func.__name__ = name
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# place_as is used by py.test to determine what source file should be
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# used for this test.
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standalone_func.place_as = func
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# Remove __wrapped__ because py.test will try to look at __wrapped__
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# to determine which parameters should be used with this test case,
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# and obviously we don't need it to do any parameterization.
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try:
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del standalone_func.__wrapped__
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except AttributeError:
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pass
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return standalone_func
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@classmethod
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def to_safe_name(cls, s):
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return str(re.sub("[^a-zA-Z0-9_]+", "_", s))
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