1058 lines
34 KiB
Python
1058 lines
34 KiB
Python
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"""Testing utilities."""
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# Copyright (c) 2011, 2012
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# Authors: Pietro Berkes,
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# Andreas Muller
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# Mathieu Blondel
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# Olivier Grisel
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# Arnaud Joly
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# Denis Engemann
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# Giorgio Patrini
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# Thierry Guillemot
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# License: BSD 3 clause
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import os
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import os.path as op
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import inspect
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import warnings
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import sys
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import functools
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import tempfile
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from subprocess import check_output, STDOUT, CalledProcessError
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from subprocess import TimeoutExpired
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import re
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import contextlib
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from collections.abc import Iterable
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from collections.abc import Sequence
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import scipy as sp
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from functools import wraps
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from inspect import signature
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import shutil
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import atexit
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import unittest
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from unittest import TestCase
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# WindowsError only exist on Windows
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try:
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WindowsError # type: ignore
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except NameError:
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WindowsError = None
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from numpy.testing import assert_allclose as np_assert_allclose
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from numpy.testing import assert_almost_equal
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from numpy.testing import assert_approx_equal
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from numpy.testing import assert_array_equal
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from numpy.testing import assert_array_almost_equal
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from numpy.testing import assert_array_less
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import numpy as np
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import joblib
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import sklearn
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from sklearn.utils import (
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IS_PYPY,
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_IS_32BIT,
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_in_unstable_openblas_configuration,
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)
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from sklearn.utils.multiclass import check_classification_targets
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from sklearn.utils.validation import (
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check_array,
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check_is_fitted,
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check_X_y,
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)
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from sklearn.utils.fixes import threadpool_info
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__all__ = [
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"assert_raises",
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"assert_raises_regexp",
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"assert_array_equal",
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"assert_almost_equal",
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"assert_array_almost_equal",
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"assert_array_less",
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"assert_approx_equal",
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"assert_allclose",
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"assert_run_python_script",
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"SkipTest",
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]
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_dummy = TestCase("__init__")
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assert_raises = _dummy.assertRaises
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SkipTest = unittest.case.SkipTest
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assert_dict_equal = _dummy.assertDictEqual
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assert_raises_regex = _dummy.assertRaisesRegex
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# assert_raises_regexp is deprecated in Python 3.4 in favor of
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# assert_raises_regex but lets keep the backward compat in scikit-learn with
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# the old name for now
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assert_raises_regexp = assert_raises_regex
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# To remove when we support numpy 1.7
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def assert_no_warnings(func, *args, **kw):
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"""
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Parameters
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----------
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func
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*args
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**kw
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"""
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# very important to avoid uncontrolled state propagation
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with warnings.catch_warnings(record=True) as w:
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warnings.simplefilter("always")
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result = func(*args, **kw)
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if hasattr(np, "FutureWarning"):
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# Filter out numpy-specific warnings in numpy >= 1.9
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w = [e for e in w if e.category is not np.VisibleDeprecationWarning]
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if len(w) > 0:
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raise AssertionError(
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"Got warnings when calling %s: [%s]"
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% (func.__name__, ", ".join(str(warning) for warning in w))
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)
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return result
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def ignore_warnings(obj=None, category=Warning):
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"""Context manager and decorator to ignore warnings.
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Note: Using this (in both variants) will clear all warnings
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from all python modules loaded. In case you need to test
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cross-module-warning-logging, this is not your tool of choice.
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Parameters
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----------
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obj : callable, default=None
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callable where you want to ignore the warnings.
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category : warning class, default=Warning
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The category to filter. If Warning, all categories will be muted.
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Examples
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--------
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>>> import warnings
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>>> from sklearn.utils._testing import ignore_warnings
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>>> with ignore_warnings():
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... warnings.warn('buhuhuhu')
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>>> def nasty_warn():
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... warnings.warn('buhuhuhu')
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... print(42)
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>>> ignore_warnings(nasty_warn)()
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42
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"""
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if isinstance(obj, type) and issubclass(obj, Warning):
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# Avoid common pitfall of passing category as the first positional
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# argument which result in the test not being run
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warning_name = obj.__name__
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raise ValueError(
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"'obj' should be a callable where you want to ignore warnings. "
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"You passed a warning class instead: 'obj={warning_name}'. "
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"If you want to pass a warning class to ignore_warnings, "
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"you should use 'category={warning_name}'".format(warning_name=warning_name)
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)
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elif callable(obj):
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return _IgnoreWarnings(category=category)(obj)
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else:
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return _IgnoreWarnings(category=category)
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class _IgnoreWarnings:
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"""Improved and simplified Python warnings context manager and decorator.
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This class allows the user to ignore the warnings raised by a function.
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Copied from Python 2.7.5 and modified as required.
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Parameters
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----------
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category : tuple of warning class, default=Warning
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The category to filter. By default, all the categories will be muted.
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"""
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def __init__(self, category):
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self._record = True
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self._module = sys.modules["warnings"]
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self._entered = False
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self.log = []
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self.category = category
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def __call__(self, fn):
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"""Decorator to catch and hide warnings without visual nesting."""
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@wraps(fn)
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def wrapper(*args, **kwargs):
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", self.category)
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return fn(*args, **kwargs)
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return wrapper
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def __repr__(self):
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args = []
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if self._record:
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args.append("record=True")
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if self._module is not sys.modules["warnings"]:
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args.append("module=%r" % self._module)
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name = type(self).__name__
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return "%s(%s)" % (name, ", ".join(args))
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def __enter__(self):
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if self._entered:
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raise RuntimeError("Cannot enter %r twice" % self)
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self._entered = True
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self._filters = self._module.filters
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self._module.filters = self._filters[:]
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self._showwarning = self._module.showwarning
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warnings.simplefilter("ignore", self.category)
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def __exit__(self, *exc_info):
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if not self._entered:
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raise RuntimeError("Cannot exit %r without entering first" % self)
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self._module.filters = self._filters
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self._module.showwarning = self._showwarning
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self.log[:] = []
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def assert_raise_message(exceptions, message, function, *args, **kwargs):
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"""Helper function to test the message raised in an exception.
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Given an exception, a callable to raise the exception, and
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a message string, tests that the correct exception is raised and
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that the message is a substring of the error thrown. Used to test
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that the specific message thrown during an exception is correct.
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Parameters
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----------
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exceptions : exception or tuple of exception
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An Exception object.
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message : str
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The error message or a substring of the error message.
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function : callable
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Callable object to raise error.
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*args : the positional arguments to `function`.
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**kwargs : the keyword arguments to `function`.
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"""
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try:
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function(*args, **kwargs)
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except exceptions as e:
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error_message = str(e)
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if message not in error_message:
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raise AssertionError(
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"Error message does not include the expected"
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" string: %r. Observed error message: %r" % (message, error_message)
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)
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else:
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# concatenate exception names
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if isinstance(exceptions, tuple):
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names = " or ".join(e.__name__ for e in exceptions)
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else:
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names = exceptions.__name__
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raise AssertionError("%s not raised by %s" % (names, function.__name__))
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def assert_allclose(
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actual, desired, rtol=None, atol=0.0, equal_nan=True, err_msg="", verbose=True
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):
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"""dtype-aware variant of numpy.testing.assert_allclose
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This variant introspects the least precise floating point dtype
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in the input argument and automatically sets the relative tolerance
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parameter to 1e-4 float32 and use 1e-7 otherwise (typically float64
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in scikit-learn).
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`atol` is always left to 0. by default. It should be adjusted manually
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to an assertion-specific value in case there are null values expected
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in `desired`.
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The aggregate tolerance is `atol + rtol * abs(desired)`.
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Parameters
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----------
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actual : array_like
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Array obtained.
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desired : array_like
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Array desired.
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rtol : float, optional, default=None
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Relative tolerance.
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If None, it is set based on the provided arrays' dtypes.
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atol : float, optional, default=0.
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Absolute tolerance.
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equal_nan : bool, optional, default=True
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If True, NaNs will compare equal.
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err_msg : str, optional, default=''
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The error message to be printed in case of failure.
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verbose : bool, optional, default=True
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If True, the conflicting values are appended to the error message.
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Raises
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------
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AssertionError
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If actual and desired are not equal up to specified precision.
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See Also
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--------
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numpy.testing.assert_allclose
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Examples
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--------
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>>> import numpy as np
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>>> from sklearn.utils._testing import assert_allclose
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>>> x = [1e-5, 1e-3, 1e-1]
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>>> y = np.arccos(np.cos(x))
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>>> assert_allclose(x, y, rtol=1e-5, atol=0)
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>>> a = np.full(shape=10, fill_value=1e-5, dtype=np.float32)
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>>> assert_allclose(a, 1e-5)
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"""
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dtypes = []
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actual, desired = np.asanyarray(actual), np.asanyarray(desired)
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dtypes = [actual.dtype, desired.dtype]
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if rtol is None:
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rtols = [1e-4 if dtype == np.float32 else 1e-7 for dtype in dtypes]
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rtol = max(rtols)
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np_assert_allclose(
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actual,
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desired,
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rtol=rtol,
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atol=atol,
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equal_nan=equal_nan,
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err_msg=err_msg,
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verbose=verbose,
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)
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def assert_allclose_dense_sparse(x, y, rtol=1e-07, atol=1e-9, err_msg=""):
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"""Assert allclose for sparse and dense data.
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Both x and y need to be either sparse or dense, they
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can't be mixed.
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Parameters
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----------
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x : {array-like, sparse matrix}
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First array to compare.
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y : {array-like, sparse matrix}
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Second array to compare.
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rtol : float, default=1e-07
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relative tolerance; see numpy.allclose.
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atol : float, default=1e-9
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absolute tolerance; see numpy.allclose. Note that the default here is
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more tolerant than the default for numpy.testing.assert_allclose, where
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atol=0.
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err_msg : str, default=''
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Error message to raise.
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"""
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if sp.sparse.issparse(x) and sp.sparse.issparse(y):
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x = x.tocsr()
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y = y.tocsr()
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x.sum_duplicates()
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y.sum_duplicates()
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assert_array_equal(x.indices, y.indices, err_msg=err_msg)
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assert_array_equal(x.indptr, y.indptr, err_msg=err_msg)
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assert_allclose(x.data, y.data, rtol=rtol, atol=atol, err_msg=err_msg)
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elif not sp.sparse.issparse(x) and not sp.sparse.issparse(y):
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# both dense
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assert_allclose(x, y, rtol=rtol, atol=atol, err_msg=err_msg)
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else:
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raise ValueError(
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"Can only compare two sparse matrices, not a sparse matrix and an array."
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)
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def set_random_state(estimator, random_state=0):
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"""Set random state of an estimator if it has the `random_state` param.
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Parameters
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----------
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estimator : object
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The estimator.
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random_state : int, RandomState instance or None, default=0
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Pseudo random number generator state.
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Pass an int for reproducible results across multiple function calls.
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See :term:`Glossary <random_state>`.
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"""
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if "random_state" in estimator.get_params():
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estimator.set_params(random_state=random_state)
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|
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|
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try:
|
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|
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import pytest
|
||
|
|
|
||
|
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skip_if_32bit = pytest.mark.skipif(_IS_32BIT, reason="skipped on 32bit platforms")
|
||
|
|
fails_if_pypy = pytest.mark.xfail(IS_PYPY, reason="not compatible with PyPy")
|
||
|
|
fails_if_unstable_openblas = pytest.mark.xfail(
|
||
|
|
_in_unstable_openblas_configuration(),
|
||
|
|
reason="OpenBLAS is unstable for this configuration",
|
||
|
|
)
|
||
|
|
skip_if_no_parallel = pytest.mark.skipif(
|
||
|
|
not joblib.parallel.mp, reason="joblib is in serial mode"
|
||
|
|
)
|
||
|
|
|
||
|
|
# Decorator for tests involving both BLAS calls and multiprocessing.
|
||
|
|
#
|
||
|
|
# Under POSIX (e.g. Linux or OSX), using multiprocessing in conjunction
|
||
|
|
# with some implementation of BLAS (or other libraries that manage an
|
||
|
|
# internal posix thread pool) can cause a crash or a freeze of the Python
|
||
|
|
# process.
|
||
|
|
#
|
||
|
|
# In practice all known packaged distributions (from Linux distros or
|
||
|
|
# Anaconda) of BLAS under Linux seems to be safe. So we this problem seems
|
||
|
|
# to only impact OSX users.
|
||
|
|
#
|
||
|
|
# This wrapper makes it possible to skip tests that can possibly cause
|
||
|
|
# this crash under OS X with.
|
||
|
|
#
|
||
|
|
# Under Python 3.4+ it is possible to use the `forkserver` start method
|
||
|
|
# for multiprocessing to avoid this issue. However it can cause pickling
|
||
|
|
# errors on interactively defined functions. It therefore not enabled by
|
||
|
|
# default.
|
||
|
|
|
||
|
|
if_safe_multiprocessing_with_blas = pytest.mark.skipif(
|
||
|
|
sys.platform == "darwin", reason="Possible multi-process bug with some BLAS"
|
||
|
|
)
|
||
|
|
except ImportError:
|
||
|
|
pass
|
||
|
|
|
||
|
|
|
||
|
|
def check_skip_network():
|
||
|
|
if int(os.environ.get("SKLEARN_SKIP_NETWORK_TESTS", 0)):
|
||
|
|
raise SkipTest("Text tutorial requires large dataset download")
|
||
|
|
|
||
|
|
|
||
|
|
def _delete_folder(folder_path, warn=False):
|
||
|
|
"""Utility function to cleanup a temporary folder if still existing.
|
||
|
|
|
||
|
|
Copy from joblib.pool (for independence).
|
||
|
|
"""
|
||
|
|
try:
|
||
|
|
if os.path.exists(folder_path):
|
||
|
|
# This can fail under windows,
|
||
|
|
# but will succeed when called by atexit
|
||
|
|
shutil.rmtree(folder_path)
|
||
|
|
except WindowsError:
|
||
|
|
if warn:
|
||
|
|
warnings.warn("Could not delete temporary folder %s" % folder_path)
|
||
|
|
|
||
|
|
|
||
|
|
class TempMemmap:
|
||
|
|
"""
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
data
|
||
|
|
mmap_mode : str, default='r'
|
||
|
|
"""
|
||
|
|
|
||
|
|
def __init__(self, data, mmap_mode="r"):
|
||
|
|
self.mmap_mode = mmap_mode
|
||
|
|
self.data = data
|
||
|
|
|
||
|
|
def __enter__(self):
|
||
|
|
data_read_only, self.temp_folder = create_memmap_backed_data(
|
||
|
|
self.data, mmap_mode=self.mmap_mode, return_folder=True
|
||
|
|
)
|
||
|
|
return data_read_only
|
||
|
|
|
||
|
|
def __exit__(self, exc_type, exc_val, exc_tb):
|
||
|
|
_delete_folder(self.temp_folder)
|
||
|
|
|
||
|
|
|
||
|
|
def _create_memmap_backed_array(array, filename, mmap_mode):
|
||
|
|
# https://numpy.org/doc/stable/reference/generated/numpy.memmap.html
|
||
|
|
fp = np.memmap(filename, dtype=array.dtype, mode="w+", shape=array.shape)
|
||
|
|
fp[:] = array[:] # write array to memmap array
|
||
|
|
fp.flush()
|
||
|
|
memmap_backed_array = np.memmap(
|
||
|
|
filename, dtype=array.dtype, mode=mmap_mode, shape=array.shape
|
||
|
|
)
|
||
|
|
return memmap_backed_array
|
||
|
|
|
||
|
|
|
||
|
|
def _create_aligned_memmap_backed_arrays(data, mmap_mode, folder):
|
||
|
|
if isinstance(data, np.ndarray):
|
||
|
|
filename = op.join(folder, "data.dat")
|
||
|
|
return _create_memmap_backed_array(data, filename, mmap_mode)
|
||
|
|
|
||
|
|
if isinstance(data, Sequence) and all(
|
||
|
|
isinstance(each, np.ndarray) for each in data
|
||
|
|
):
|
||
|
|
return [
|
||
|
|
_create_memmap_backed_array(
|
||
|
|
array, op.join(folder, f"data{index}.dat"), mmap_mode
|
||
|
|
)
|
||
|
|
for index, array in enumerate(data)
|
||
|
|
]
|
||
|
|
|
||
|
|
raise ValueError(
|
||
|
|
"When creating aligned memmap-backed arrays, input must be a single array or a"
|
||
|
|
" sequence of arrays"
|
||
|
|
)
|
||
|
|
|
||
|
|
|
||
|
|
def create_memmap_backed_data(data, mmap_mode="r", return_folder=False, aligned=False):
|
||
|
|
"""
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
data
|
||
|
|
mmap_mode : str, default='r'
|
||
|
|
return_folder : bool, default=False
|
||
|
|
aligned : bool, default=False
|
||
|
|
If True, if input is a single numpy array and if the input array is aligned,
|
||
|
|
the memory mapped array will also be aligned. This is a workaround for
|
||
|
|
https://github.com/joblib/joblib/issues/563.
|
||
|
|
"""
|
||
|
|
temp_folder = tempfile.mkdtemp(prefix="sklearn_testing_")
|
||
|
|
atexit.register(functools.partial(_delete_folder, temp_folder, warn=True))
|
||
|
|
# OpenBLAS is known to segfault with unaligned data on the Prescott
|
||
|
|
# architecture so force aligned=True on Prescott. For more details, see:
|
||
|
|
# https://github.com/scipy/scipy/issues/14886
|
||
|
|
has_prescott_openblas = any(
|
||
|
|
True
|
||
|
|
for info in threadpool_info()
|
||
|
|
if info["internal_api"] == "openblas"
|
||
|
|
# Prudently assume Prescott might be the architecture if it is unknown.
|
||
|
|
and info.get("architecture", "prescott").lower() == "prescott"
|
||
|
|
)
|
||
|
|
if has_prescott_openblas:
|
||
|
|
aligned = True
|
||
|
|
|
||
|
|
if aligned:
|
||
|
|
memmap_backed_data = _create_aligned_memmap_backed_arrays(
|
||
|
|
data, mmap_mode, temp_folder
|
||
|
|
)
|
||
|
|
else:
|
||
|
|
filename = op.join(temp_folder, "data.pkl")
|
||
|
|
joblib.dump(data, filename)
|
||
|
|
memmap_backed_data = joblib.load(filename, mmap_mode=mmap_mode)
|
||
|
|
result = (
|
||
|
|
memmap_backed_data if not return_folder else (memmap_backed_data, temp_folder)
|
||
|
|
)
|
||
|
|
return result
|
||
|
|
|
||
|
|
|
||
|
|
# Utils to test docstrings
|
||
|
|
|
||
|
|
|
||
|
|
def _get_args(function, varargs=False):
|
||
|
|
"""Helper to get function arguments."""
|
||
|
|
|
||
|
|
try:
|
||
|
|
params = signature(function).parameters
|
||
|
|
except ValueError:
|
||
|
|
# Error on builtin C function
|
||
|
|
return []
|
||
|
|
args = [
|
||
|
|
key
|
||
|
|
for key, param in params.items()
|
||
|
|
if param.kind not in (param.VAR_POSITIONAL, param.VAR_KEYWORD)
|
||
|
|
]
|
||
|
|
if varargs:
|
||
|
|
varargs = [
|
||
|
|
param.name
|
||
|
|
for param in params.values()
|
||
|
|
if param.kind == param.VAR_POSITIONAL
|
||
|
|
]
|
||
|
|
if len(varargs) == 0:
|
||
|
|
varargs = None
|
||
|
|
return args, varargs
|
||
|
|
else:
|
||
|
|
return args
|
||
|
|
|
||
|
|
|
||
|
|
def _get_func_name(func):
|
||
|
|
"""Get function full name.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
func : callable
|
||
|
|
The function object.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
name : str
|
||
|
|
The function name.
|
||
|
|
"""
|
||
|
|
parts = []
|
||
|
|
module = inspect.getmodule(func)
|
||
|
|
if module:
|
||
|
|
parts.append(module.__name__)
|
||
|
|
|
||
|
|
qualname = func.__qualname__
|
||
|
|
if qualname != func.__name__:
|
||
|
|
parts.append(qualname[: qualname.find(".")])
|
||
|
|
|
||
|
|
parts.append(func.__name__)
|
||
|
|
return ".".join(parts)
|
||
|
|
|
||
|
|
|
||
|
|
def check_docstring_parameters(func, doc=None, ignore=None):
|
||
|
|
"""Helper to check docstring.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
func : callable
|
||
|
|
The function object to test.
|
||
|
|
doc : str, default=None
|
||
|
|
Docstring if it is passed manually to the test.
|
||
|
|
ignore : list, default=None
|
||
|
|
Parameters to ignore.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
incorrect : list
|
||
|
|
A list of string describing the incorrect results.
|
||
|
|
"""
|
||
|
|
from numpydoc import docscrape
|
||
|
|
|
||
|
|
incorrect = []
|
||
|
|
ignore = [] if ignore is None else ignore
|
||
|
|
|
||
|
|
func_name = _get_func_name(func)
|
||
|
|
if not func_name.startswith("sklearn.") or func_name.startswith(
|
||
|
|
"sklearn.externals"
|
||
|
|
):
|
||
|
|
return incorrect
|
||
|
|
# Don't check docstring for property-functions
|
||
|
|
if inspect.isdatadescriptor(func):
|
||
|
|
return incorrect
|
||
|
|
# Don't check docstring for setup / teardown pytest functions
|
||
|
|
if func_name.split(".")[-1] in ("setup_module", "teardown_module"):
|
||
|
|
return incorrect
|
||
|
|
# Dont check estimator_checks module
|
||
|
|
if func_name.split(".")[2] == "estimator_checks":
|
||
|
|
return incorrect
|
||
|
|
# Get the arguments from the function signature
|
||
|
|
param_signature = list(filter(lambda x: x not in ignore, _get_args(func)))
|
||
|
|
# drop self
|
||
|
|
if len(param_signature) > 0 and param_signature[0] == "self":
|
||
|
|
param_signature.remove("self")
|
||
|
|
|
||
|
|
# Analyze function's docstring
|
||
|
|
if doc is None:
|
||
|
|
records = []
|
||
|
|
with warnings.catch_warnings(record=True):
|
||
|
|
warnings.simplefilter("error", UserWarning)
|
||
|
|
try:
|
||
|
|
doc = docscrape.FunctionDoc(func)
|
||
|
|
except UserWarning as exp:
|
||
|
|
if "potentially wrong underline length" in str(exp):
|
||
|
|
# Catch warning raised as of numpydoc 1.2 when
|
||
|
|
# the underline length for a section of a docstring
|
||
|
|
# is not consistent.
|
||
|
|
message = str(exp).split("\n")[:3]
|
||
|
|
incorrect += [f"In function: {func_name}"] + message
|
||
|
|
return incorrect
|
||
|
|
records.append(str(exp))
|
||
|
|
except Exception as exp:
|
||
|
|
incorrect += [func_name + " parsing error: " + str(exp)]
|
||
|
|
return incorrect
|
||
|
|
if len(records):
|
||
|
|
raise RuntimeError("Error for %s:\n%s" % (func_name, records[0]))
|
||
|
|
|
||
|
|
param_docs = []
|
||
|
|
for name, type_definition, param_doc in doc["Parameters"]:
|
||
|
|
# Type hints are empty only if parameter name ended with :
|
||
|
|
if not type_definition.strip():
|
||
|
|
if ":" in name and name[: name.index(":")][-1:].strip():
|
||
|
|
incorrect += [
|
||
|
|
func_name
|
||
|
|
+ " There was no space between the param name and colon (%r)" % name
|
||
|
|
]
|
||
|
|
elif name.rstrip().endswith(":"):
|
||
|
|
incorrect += [
|
||
|
|
func_name
|
||
|
|
+ " Parameter %r has an empty type spec. Remove the colon"
|
||
|
|
% (name.lstrip())
|
||
|
|
]
|
||
|
|
|
||
|
|
# Create a list of parameters to compare with the parameters gotten
|
||
|
|
# from the func signature
|
||
|
|
if "*" not in name:
|
||
|
|
param_docs.append(name.split(":")[0].strip("` "))
|
||
|
|
|
||
|
|
# If one of the docstring's parameters had an error then return that
|
||
|
|
# incorrect message
|
||
|
|
if len(incorrect) > 0:
|
||
|
|
return incorrect
|
||
|
|
|
||
|
|
# Remove the parameters that should be ignored from list
|
||
|
|
param_docs = list(filter(lambda x: x not in ignore, param_docs))
|
||
|
|
|
||
|
|
# The following is derived from pytest, Copyright (c) 2004-2017 Holger
|
||
|
|
# Krekel and others, Licensed under MIT License. See
|
||
|
|
# https://github.com/pytest-dev/pytest
|
||
|
|
|
||
|
|
message = []
|
||
|
|
for i in range(min(len(param_docs), len(param_signature))):
|
||
|
|
if param_signature[i] != param_docs[i]:
|
||
|
|
message += [
|
||
|
|
"There's a parameter name mismatch in function"
|
||
|
|
" docstring w.r.t. function signature, at index %s"
|
||
|
|
" diff: %r != %r" % (i, param_signature[i], param_docs[i])
|
||
|
|
]
|
||
|
|
break
|
||
|
|
if len(param_signature) > len(param_docs):
|
||
|
|
message += [
|
||
|
|
"Parameters in function docstring have less items w.r.t."
|
||
|
|
" function signature, first missing item: %s"
|
||
|
|
% param_signature[len(param_docs)]
|
||
|
|
]
|
||
|
|
|
||
|
|
elif len(param_signature) < len(param_docs):
|
||
|
|
message += [
|
||
|
|
"Parameters in function docstring have more items w.r.t."
|
||
|
|
" function signature, first extra item: %s"
|
||
|
|
% param_docs[len(param_signature)]
|
||
|
|
]
|
||
|
|
|
||
|
|
# If there wasn't any difference in the parameters themselves between
|
||
|
|
# docstring and signature including having the same length then return
|
||
|
|
# empty list
|
||
|
|
if len(message) == 0:
|
||
|
|
return []
|
||
|
|
|
||
|
|
import difflib
|
||
|
|
import pprint
|
||
|
|
|
||
|
|
param_docs_formatted = pprint.pformat(param_docs).splitlines()
|
||
|
|
param_signature_formatted = pprint.pformat(param_signature).splitlines()
|
||
|
|
|
||
|
|
message += ["Full diff:"]
|
||
|
|
|
||
|
|
message.extend(
|
||
|
|
line.strip()
|
||
|
|
for line in difflib.ndiff(param_signature_formatted, param_docs_formatted)
|
||
|
|
)
|
||
|
|
|
||
|
|
incorrect.extend(message)
|
||
|
|
|
||
|
|
# Prepend function name
|
||
|
|
incorrect = ["In function: " + func_name] + incorrect
|
||
|
|
|
||
|
|
return incorrect
|
||
|
|
|
||
|
|
|
||
|
|
def assert_run_python_script(source_code, timeout=60):
|
||
|
|
"""Utility to check assertions in an independent Python subprocess.
|
||
|
|
|
||
|
|
The script provided in the source code should return 0 and not print
|
||
|
|
anything on stderr or stdout.
|
||
|
|
|
||
|
|
This is a port from cloudpickle https://github.com/cloudpipe/cloudpickle
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
source_code : str
|
||
|
|
The Python source code to execute.
|
||
|
|
timeout : int, default=60
|
||
|
|
Time in seconds before timeout.
|
||
|
|
"""
|
||
|
|
fd, source_file = tempfile.mkstemp(suffix="_src_test_sklearn.py")
|
||
|
|
os.close(fd)
|
||
|
|
try:
|
||
|
|
with open(source_file, "wb") as f:
|
||
|
|
f.write(source_code.encode("utf-8"))
|
||
|
|
cmd = [sys.executable, source_file]
|
||
|
|
cwd = op.normpath(op.join(op.dirname(sklearn.__file__), ".."))
|
||
|
|
env = os.environ.copy()
|
||
|
|
try:
|
||
|
|
env["PYTHONPATH"] = os.pathsep.join([cwd, env["PYTHONPATH"]])
|
||
|
|
except KeyError:
|
||
|
|
env["PYTHONPATH"] = cwd
|
||
|
|
kwargs = {"cwd": cwd, "stderr": STDOUT, "env": env}
|
||
|
|
# If coverage is running, pass the config file to the subprocess
|
||
|
|
coverage_rc = os.environ.get("COVERAGE_PROCESS_START")
|
||
|
|
if coverage_rc:
|
||
|
|
kwargs["env"]["COVERAGE_PROCESS_START"] = coverage_rc
|
||
|
|
|
||
|
|
kwargs["timeout"] = timeout
|
||
|
|
try:
|
||
|
|
try:
|
||
|
|
out = check_output(cmd, **kwargs)
|
||
|
|
except CalledProcessError as e:
|
||
|
|
raise RuntimeError(
|
||
|
|
"script errored with output:\n%s" % e.output.decode("utf-8")
|
||
|
|
)
|
||
|
|
if out != b"":
|
||
|
|
raise AssertionError(out.decode("utf-8"))
|
||
|
|
except TimeoutExpired as e:
|
||
|
|
raise RuntimeError(
|
||
|
|
"script timeout, output so far:\n%s" % e.output.decode("utf-8")
|
||
|
|
)
|
||
|
|
finally:
|
||
|
|
os.unlink(source_file)
|
||
|
|
|
||
|
|
|
||
|
|
def _convert_container(container, constructor_name, columns_name=None, dtype=None):
|
||
|
|
"""Convert a given container to a specific array-like with a dtype.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
container : array-like
|
||
|
|
The container to convert.
|
||
|
|
constructor_name : {"list", "tuple", "array", "sparse", "dataframe", \
|
||
|
|
"series", "index", "slice", "sparse_csr", "sparse_csc"}
|
||
|
|
The type of the returned container.
|
||
|
|
columns_name : index or array-like, default=None
|
||
|
|
For pandas container supporting `columns_names`, it will affect
|
||
|
|
specific names.
|
||
|
|
dtype : dtype, default=None
|
||
|
|
Force the dtype of the container. Does not apply to `"slice"`
|
||
|
|
container.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
converted_container
|
||
|
|
"""
|
||
|
|
if constructor_name == "list":
|
||
|
|
if dtype is None:
|
||
|
|
return list(container)
|
||
|
|
else:
|
||
|
|
return np.asarray(container, dtype=dtype).tolist()
|
||
|
|
elif constructor_name == "tuple":
|
||
|
|
if dtype is None:
|
||
|
|
return tuple(container)
|
||
|
|
else:
|
||
|
|
return tuple(np.asarray(container, dtype=dtype).tolist())
|
||
|
|
elif constructor_name == "array":
|
||
|
|
return np.asarray(container, dtype=dtype)
|
||
|
|
elif constructor_name == "sparse":
|
||
|
|
return sp.sparse.csr_matrix(container, dtype=dtype)
|
||
|
|
elif constructor_name == "dataframe":
|
||
|
|
pd = pytest.importorskip("pandas")
|
||
|
|
return pd.DataFrame(container, columns=columns_name, dtype=dtype)
|
||
|
|
elif constructor_name == "series":
|
||
|
|
pd = pytest.importorskip("pandas")
|
||
|
|
return pd.Series(container, dtype=dtype)
|
||
|
|
elif constructor_name == "index":
|
||
|
|
pd = pytest.importorskip("pandas")
|
||
|
|
return pd.Index(container, dtype=dtype)
|
||
|
|
elif constructor_name == "slice":
|
||
|
|
return slice(container[0], container[1])
|
||
|
|
elif constructor_name == "sparse_csr":
|
||
|
|
return sp.sparse.csr_matrix(container, dtype=dtype)
|
||
|
|
elif constructor_name == "sparse_csc":
|
||
|
|
return sp.sparse.csc_matrix(container, dtype=dtype)
|
||
|
|
|
||
|
|
|
||
|
|
def raises(expected_exc_type, match=None, may_pass=False, err_msg=None):
|
||
|
|
"""Context manager to ensure exceptions are raised within a code block.
|
||
|
|
|
||
|
|
This is similar to and inspired from pytest.raises, but supports a few
|
||
|
|
other cases.
|
||
|
|
|
||
|
|
This is only intended to be used in estimator_checks.py where we don't
|
||
|
|
want to use pytest. In the rest of the code base, just use pytest.raises
|
||
|
|
instead.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
excepted_exc_type : Exception or list of Exception
|
||
|
|
The exception that should be raised by the block. If a list, the block
|
||
|
|
should raise one of the exceptions.
|
||
|
|
match : str or list of str, default=None
|
||
|
|
A regex that the exception message should match. If a list, one of
|
||
|
|
the entries must match. If None, match isn't enforced.
|
||
|
|
may_pass : bool, default=False
|
||
|
|
If True, the block is allowed to not raise an exception. Useful in
|
||
|
|
cases where some estimators may support a feature but others must
|
||
|
|
fail with an appropriate error message. By default, the context
|
||
|
|
manager will raise an exception if the block does not raise an
|
||
|
|
exception.
|
||
|
|
err_msg : str, default=None
|
||
|
|
If the context manager fails (e.g. the block fails to raise the
|
||
|
|
proper exception, or fails to match), then an AssertionError is
|
||
|
|
raised with this message. By default, an AssertionError is raised
|
||
|
|
with a default error message (depends on the kind of failure). Use
|
||
|
|
this to indicate how users should fix their estimators to pass the
|
||
|
|
checks.
|
||
|
|
|
||
|
|
Attributes
|
||
|
|
----------
|
||
|
|
raised_and_matched : bool
|
||
|
|
True if an exception was raised and a match was found, False otherwise.
|
||
|
|
"""
|
||
|
|
return _Raises(expected_exc_type, match, may_pass, err_msg)
|
||
|
|
|
||
|
|
|
||
|
|
class _Raises(contextlib.AbstractContextManager):
|
||
|
|
# see raises() for parameters
|
||
|
|
def __init__(self, expected_exc_type, match, may_pass, err_msg):
|
||
|
|
self.expected_exc_types = (
|
||
|
|
expected_exc_type
|
||
|
|
if isinstance(expected_exc_type, Iterable)
|
||
|
|
else [expected_exc_type]
|
||
|
|
)
|
||
|
|
self.matches = [match] if isinstance(match, str) else match
|
||
|
|
self.may_pass = may_pass
|
||
|
|
self.err_msg = err_msg
|
||
|
|
self.raised_and_matched = False
|
||
|
|
|
||
|
|
def __exit__(self, exc_type, exc_value, _):
|
||
|
|
# see
|
||
|
|
# https://docs.python.org/2.5/whatsnew/pep-343.html#SECTION000910000000000000000
|
||
|
|
|
||
|
|
if exc_type is None: # No exception was raised in the block
|
||
|
|
if self.may_pass:
|
||
|
|
return True # CM is happy
|
||
|
|
else:
|
||
|
|
err_msg = self.err_msg or f"Did not raise: {self.expected_exc_types}"
|
||
|
|
raise AssertionError(err_msg)
|
||
|
|
|
||
|
|
if not any(
|
||
|
|
issubclass(exc_type, expected_type)
|
||
|
|
for expected_type in self.expected_exc_types
|
||
|
|
):
|
||
|
|
if self.err_msg is not None:
|
||
|
|
raise AssertionError(self.err_msg) from exc_value
|
||
|
|
else:
|
||
|
|
return False # will re-raise the original exception
|
||
|
|
|
||
|
|
if self.matches is not None:
|
||
|
|
err_msg = self.err_msg or (
|
||
|
|
"The error message should contain one of the following "
|
||
|
|
"patterns:\n{}\nGot {}".format("\n".join(self.matches), str(exc_value))
|
||
|
|
)
|
||
|
|
if not any(re.search(match, str(exc_value)) for match in self.matches):
|
||
|
|
raise AssertionError(err_msg) from exc_value
|
||
|
|
self.raised_and_matched = True
|
||
|
|
|
||
|
|
return True
|
||
|
|
|
||
|
|
|
||
|
|
class MinimalClassifier:
|
||
|
|
"""Minimal classifier implementation with inheriting from BaseEstimator.
|
||
|
|
|
||
|
|
This estimator should be tested with:
|
||
|
|
|
||
|
|
* `check_estimator` in `test_estimator_checks.py`;
|
||
|
|
* within a `Pipeline` in `test_pipeline.py`;
|
||
|
|
* within a `SearchCV` in `test_search.py`.
|
||
|
|
"""
|
||
|
|
|
||
|
|
_estimator_type = "classifier"
|
||
|
|
|
||
|
|
def __init__(self, param=None):
|
||
|
|
self.param = param
|
||
|
|
|
||
|
|
def get_params(self, deep=True):
|
||
|
|
return {"param": self.param}
|
||
|
|
|
||
|
|
def set_params(self, **params):
|
||
|
|
for key, value in params.items():
|
||
|
|
setattr(self, key, value)
|
||
|
|
return self
|
||
|
|
|
||
|
|
def fit(self, X, y):
|
||
|
|
X, y = check_X_y(X, y)
|
||
|
|
check_classification_targets(y)
|
||
|
|
self.classes_, counts = np.unique(y, return_counts=True)
|
||
|
|
self._most_frequent_class_idx = counts.argmax()
|
||
|
|
return self
|
||
|
|
|
||
|
|
def predict_proba(self, X):
|
||
|
|
check_is_fitted(self)
|
||
|
|
X = check_array(X)
|
||
|
|
proba_shape = (X.shape[0], self.classes_.size)
|
||
|
|
y_proba = np.zeros(shape=proba_shape, dtype=np.float64)
|
||
|
|
y_proba[:, self._most_frequent_class_idx] = 1.0
|
||
|
|
return y_proba
|
||
|
|
|
||
|
|
def predict(self, X):
|
||
|
|
y_proba = self.predict_proba(X)
|
||
|
|
y_pred = y_proba.argmax(axis=1)
|
||
|
|
return self.classes_[y_pred]
|
||
|
|
|
||
|
|
def score(self, X, y):
|
||
|
|
from sklearn.metrics import accuracy_score
|
||
|
|
|
||
|
|
return accuracy_score(y, self.predict(X))
|
||
|
|
|
||
|
|
|
||
|
|
class MinimalRegressor:
|
||
|
|
"""Minimal regressor implementation with inheriting from BaseEstimator.
|
||
|
|
|
||
|
|
This estimator should be tested with:
|
||
|
|
|
||
|
|
* `check_estimator` in `test_estimator_checks.py`;
|
||
|
|
* within a `Pipeline` in `test_pipeline.py`;
|
||
|
|
* within a `SearchCV` in `test_search.py`.
|
||
|
|
"""
|
||
|
|
|
||
|
|
_estimator_type = "regressor"
|
||
|
|
|
||
|
|
def __init__(self, param=None):
|
||
|
|
self.param = param
|
||
|
|
|
||
|
|
def get_params(self, deep=True):
|
||
|
|
return {"param": self.param}
|
||
|
|
|
||
|
|
def set_params(self, **params):
|
||
|
|
for key, value in params.items():
|
||
|
|
setattr(self, key, value)
|
||
|
|
return self
|
||
|
|
|
||
|
|
def fit(self, X, y):
|
||
|
|
X, y = check_X_y(X, y)
|
||
|
|
self.is_fitted_ = True
|
||
|
|
self._mean = np.mean(y)
|
||
|
|
return self
|
||
|
|
|
||
|
|
def predict(self, X):
|
||
|
|
check_is_fitted(self)
|
||
|
|
X = check_array(X)
|
||
|
|
return np.ones(shape=(X.shape[0],)) * self._mean
|
||
|
|
|
||
|
|
def score(self, X, y):
|
||
|
|
from sklearn.metrics import r2_score
|
||
|
|
|
||
|
|
return r2_score(y, self.predict(X))
|
||
|
|
|
||
|
|
|
||
|
|
class MinimalTransformer:
|
||
|
|
"""Minimal transformer implementation with inheriting from
|
||
|
|
BaseEstimator.
|
||
|
|
|
||
|
|
This estimator should be tested with:
|
||
|
|
|
||
|
|
* `check_estimator` in `test_estimator_checks.py`;
|
||
|
|
* within a `Pipeline` in `test_pipeline.py`;
|
||
|
|
* within a `SearchCV` in `test_search.py`.
|
||
|
|
"""
|
||
|
|
|
||
|
|
def __init__(self, param=None):
|
||
|
|
self.param = param
|
||
|
|
|
||
|
|
def get_params(self, deep=True):
|
||
|
|
return {"param": self.param}
|
||
|
|
|
||
|
|
def set_params(self, **params):
|
||
|
|
for key, value in params.items():
|
||
|
|
setattr(self, key, value)
|
||
|
|
return self
|
||
|
|
|
||
|
|
def fit(self, X, y=None):
|
||
|
|
check_array(X)
|
||
|
|
self.is_fitted_ = True
|
||
|
|
return self
|
||
|
|
|
||
|
|
def transform(self, X, y=None):
|
||
|
|
check_is_fitted(self)
|
||
|
|
X = check_array(X)
|
||
|
|
return X
|
||
|
|
|
||
|
|
def fit_transform(self, X, y=None):
|
||
|
|
return self.fit(X, y).transform(X, y)
|