Added _util.py + fixed a bug in test_fit.py
Per A Brodtkorb
9 years ago
parent
e73624161c
commit
df78c0e728
@ -0,0 +1,267 @@
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from __future__ import division, print_function, absolute_import
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import functools
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import operator
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import sys
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import warnings
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import numbers
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from collections import namedtuple
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import inspect
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import numpy as np
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def _valarray(shape, value=np.nan, typecode=None):
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"""Return an array of all value.
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"""
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out = np.ones(shape, dtype=bool) * value
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if typecode is not None:
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out = out.astype(typecode)
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if not isinstance(out, np.ndarray):
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out = np.asarray(out)
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return out
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def _lazywhere(cond, arrays, f, fillvalue=None, f2=None):
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"""
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np.where(cond, x, fillvalue) always evaluates x even where cond is False.
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This one only evaluates f(arr1[cond], arr2[cond], ...).
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For example,
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>>> a, b = np.array([1, 2, 3, 4]), np.array([5, 6, 7, 8])
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>>> def f(a, b):
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return a*b
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>>> _lazywhere(a > 2, (a, b), f, np.nan)
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array([ nan, nan, 21., 32.])
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Notice it assumes that all `arrays` are of the same shape, or can be
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broadcasted together.
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"""
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if fillvalue is None:
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if f2 is None:
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raise ValueError("One of (fillvalue, f2) must be given.")
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else:
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fillvalue = np.nan
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else:
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if f2 is not None:
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raise ValueError("Only one of (fillvalue, f2) can be given.")
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arrays = np.broadcast_arrays(*arrays)
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temp = tuple(np.extract(cond, arr) for arr in arrays)
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out = _valarray(np.shape(arrays[0]), value=fillvalue)
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np.place(out, cond, f(*temp))
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if f2 is not None:
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temp = tuple(np.extract(~cond, arr) for arr in arrays)
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np.place(out, ~cond, f2(*temp))
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return out
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def _aligned_zeros(shape, dtype=float, order="C", align=None):
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"""Allocate a new ndarray with aligned memory.
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Primary use case for this currently is working around a f2py issue
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in Numpy 1.9.1, where dtype.alignment is such that np.zeros() does
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not necessarily create arrays aligned up to it.
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"""
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dtype = np.dtype(dtype)
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if align is None:
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align = dtype.alignment
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if not hasattr(shape, '__len__'):
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shape = (shape,)
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size = functools.reduce(operator.mul, shape) * dtype.itemsize
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buf = np.empty(size + align + 1, np.uint8)
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offset = buf.__array_interface__['data'][0] % align
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if offset != 0:
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offset = align - offset
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# Note: slices producing 0-size arrays do not necessarily change
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# data pointer --- so we use and allocate size+1
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buf = buf[offset:offset+size+1][:-1]
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data = np.ndarray(shape, dtype, buf, order=order)
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data.fill(0)
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return data
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class DeprecatedImport(object):
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"""
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Deprecated import, with redirection + warning.
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Examples
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--------
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Suppose you previously had in some module::
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from foo import spam
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If this has to be deprecated, do::
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spam = DeprecatedImport("foo.spam", "baz")
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to redirect users to use "baz" module instead.
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"""
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def __init__(self, old_module_name, new_module_name):
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self._old_name = old_module_name
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self._new_name = new_module_name
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__import__(self._new_name)
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self._mod = sys.modules[self._new_name]
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def __dir__(self):
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return dir(self._mod)
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def __getattr__(self, name):
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warnings.warn("Module %s is deprecated, use %s instead"
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% (self._old_name, self._new_name),
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DeprecationWarning)
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return getattr(self._mod, name)
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# copy-pasted from scikit-learn utils/validation.py
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def check_random_state(seed):
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"""Turn seed into a np.random.RandomState instance
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If seed is None (or np.random), return the RandomState singleton used
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by np.random.
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If seed is an int, return a new RandomState instance seeded with seed.
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If seed is already a RandomState instance, return it.
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Otherwise raise ValueError.
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"""
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if seed is None or seed is np.random:
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return np.random.mtrand._rand
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if isinstance(seed, (numbers.Integral, np.integer)):
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return np.random.RandomState(seed)
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if isinstance(seed, np.random.RandomState):
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return seed
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raise ValueError('%r cannot be used to seed a numpy.random.RandomState'
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' instance' % seed)
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def _asarray_validated(a, check_finite=True,
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sparse_ok=False, objects_ok=False, mask_ok=False,
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as_inexact=False):
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"""
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Helper function for scipy argument validation.
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Many scipy linear algebra functions do support arbitrary array-like
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input arguments. Examples of commonly unsupported inputs include
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matrices containing inf/nan, sparse matrix representations, and
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matrices with complicated elements.
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Parameters
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----------
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a : array_like
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The array-like input.
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check_finite : bool, optional
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Whether to check that the input matrices contain only finite numbers.
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Disabling may give a performance gain, but may result in problems
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(crashes, non-termination) if the inputs do contain infinities or NaNs.
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Default: True
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sparse_ok : bool, optional
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True if scipy sparse matrices are allowed.
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objects_ok : bool, optional
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True if arrays with dype('O') are allowed.
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mask_ok : bool, optional
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True if masked arrays are allowed.
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as_inexact : bool, optional
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True to convert the input array to a np.inexact dtype.
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Returns
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-------
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ret : ndarray
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The converted validated array.
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"""
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if not sparse_ok:
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import scipy.sparse
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if scipy.sparse.issparse(a):
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msg = ('Sparse matrices are not supported by this function. '
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'Perhaps one of the scipy.sparse.linalg functions '
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'would work instead.')
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raise ValueError(msg)
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if not mask_ok:
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if np.ma.isMaskedArray(a):
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raise ValueError('masked arrays are not supported')
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toarray = np.asarray_chkfinite if check_finite else np.asarray
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a = toarray(a)
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if not objects_ok:
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if a.dtype is np.dtype('O'):
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raise ValueError('object arrays are not supported')
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if as_inexact:
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if not np.issubdtype(a.dtype, np.inexact):
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a = toarray(a, dtype=np.float_)
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return a
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# Add a replacement for inspect.getargspec() which is deprecated in python 3.5
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# The version below is borrowed from Django,
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# https://github.com/django/django/pull/4846
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# Note an inconsistency between inspect.getargspec(func) and
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# inspect.signature(func). If `func` is a bound method, the latter does *not*
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# list `self` as a first argument, while the former *does*.
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# Hence cook up a common ground replacement: `getargspec_no_self` which
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# mimics `inspect.getargspec` but does not list `self`.
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#
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# This way, the caller code does not need to know whether it uses a legacy
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# .getargspec or bright and shiny .signature.
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try:
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# is it python 3.3 or higher?
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inspect.signature # @UndefinedVariable
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# Apparently, yes. Wrap inspect.signature
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ArgSpec = namedtuple('ArgSpec', ['args', 'varargs', 'keywords', 'defaults'])
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def getargspec_no_self(func):
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"""inspect.getargspec replacement using inspect.signature.
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inspect.getargspec is deprecated in python 3. This is a replacement
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based on the (new in python 3.3) `inspect.signature`.
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Parameters
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----------
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func : callable
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A callable to inspect
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Returns
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-------
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argspec : ArgSpec(args, varargs, varkw, defaults)
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This is similar to the result of inspect.getargspec(func) under
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python 2.x.
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NOTE: if the first argument of `func` is self, it is *not*, I repeat
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*not* included in argspec.args.
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This is done for consistency between inspect.getargspec() under
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python 2.x, and inspect.signature() under python 3.x.
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"""
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sig = inspect.signature(func)
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args = [
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p.name for p in sig.parameters.values()
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if p.kind == inspect.Parameter.POSITIONAL_OR_KEYWORD
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]
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varargs = [
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p.name for p in sig.parameters.values()
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if p.kind == inspect.Parameter.VAR_POSITIONAL
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]
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varargs = varargs[0] if varargs else None
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varkw = [
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p.name for p in sig.parameters.values()
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if p.kind == inspect.Parameter.VAR_KEYWORD
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]
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varkw = varkw[0] if varkw else None
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defaults = [
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p.default for p in sig.parameters.values()
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if (p.kind == inspect.Parameter.POSITIONAL_OR_KEYWORD and
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p.default is not p.empty)
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] or None
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return ArgSpec(args, varargs, varkw, defaults)
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except AttributeError:
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# python 2.x
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def getargspec_no_self(func):
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"""inspect.getargspec replacement for compatibility with python 3.x.
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inspect.getargspec is deprecated in python 3. This wraps it, and
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*removes* `self` from the argument list of `func`, if present.
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This is done for forward compatibility with python 3.
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Parameters
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----------
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func : callable
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A callable to inspect
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Returns
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-------
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argspec : ArgSpec(args, varargs, varkw, defaults)
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This is similar to the result of inspect.getargspec(func) under
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python 2.x.
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NOTE: if the first argument of `func` is self, it is *not*, I repeat
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*not* included in argspec.args.
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This is done for consistency between inspect.getargspec() under
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python 2.x, and inspect.signature() under python 3.x.
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"""
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argspec = inspect.getargspec(func)
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if argspec.args[0] == 'self':
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argspec.args.pop(0)
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return argspec
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