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639 lines
23 KiB
639 lines
23 KiB
from multiprocessing import Pool
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from multiprocessing.pool import Pool as PWL
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import re
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import math
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import functools
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from fractions import Fraction
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import numpy as np
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from numpy.testing import assert_equal, assert_
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import pytest
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from pytest import raises as assert_raises
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from scipy.conftest import skip_xp_invalid_arg
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from scipy._lib._array_api import xp_assert_equal
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from scipy._lib._util import (_aligned_zeros, check_random_state, MapWrapper,
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getfullargspec_no_self, FullArgSpec,
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rng_integers, _validate_int, _rename_parameter,
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_contains_nan, _rng_html_rewrite, _workers_wrapper)
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import scipy._lib.array_api_extra as xpx
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from scipy._lib.array_api_extra.testing import lazy_xp_function
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from scipy import cluster, interpolate, linalg, optimize, sparse, spatial, stats
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lazy_xp_function(_contains_nan)
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@pytest.mark.slow
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def test__aligned_zeros():
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niter = 10
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def check(shape, dtype, order, align):
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err_msg = repr((shape, dtype, order, align))
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x = _aligned_zeros(shape, dtype, order, align=align)
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if align is None:
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align = np.dtype(dtype).alignment
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assert_equal(x.__array_interface__['data'][0] % align, 0)
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if hasattr(shape, '__len__'):
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assert_equal(x.shape, shape, err_msg)
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else:
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assert_equal(x.shape, (shape,), err_msg)
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assert_equal(x.dtype, dtype)
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if order == "C":
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assert_(x.flags.c_contiguous, err_msg)
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elif order == "F":
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if x.size > 0:
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# Size-0 arrays get invalid flags on NumPy 1.5
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assert_(x.flags.f_contiguous, err_msg)
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elif order is None:
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assert_(x.flags.c_contiguous, err_msg)
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else:
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raise ValueError()
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# try various alignments
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for align in [1, 2, 3, 4, 8, 16, 32, 64, None]:
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for n in [0, 1, 3, 11]:
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for order in ["C", "F", None]:
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for dtype in [np.uint8, np.float64]:
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for shape in [n, (1, 2, 3, n)]:
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for j in range(niter):
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check(shape, dtype, order, align)
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def test_check_random_state():
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# If seed is None, return the RandomState singleton used 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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rsi = check_random_state(1)
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assert_equal(type(rsi), np.random.RandomState)
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rsi = check_random_state(rsi)
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assert_equal(type(rsi), np.random.RandomState)
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rsi = check_random_state(None)
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assert_equal(type(rsi), np.random.RandomState)
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assert_raises(ValueError, check_random_state, 'a')
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rg = np.random.Generator(np.random.PCG64())
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rsi = check_random_state(rg)
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assert_equal(type(rsi), np.random.Generator)
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def test_getfullargspec_no_self():
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p = MapWrapper(1)
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argspec = getfullargspec_no_self(p.__init__)
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assert_equal(argspec, FullArgSpec(['pool'], None, None, (1,), [],
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None, {}))
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argspec = getfullargspec_no_self(p.__call__)
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assert_equal(argspec, FullArgSpec(['func', 'iterable'], None, None, None,
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[], None, {}))
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class _rv_generic:
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def _rvs(self, a, b=2, c=3, *args, size=None, **kwargs):
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return None
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rv_obj = _rv_generic()
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argspec = getfullargspec_no_self(rv_obj._rvs)
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assert_equal(argspec, FullArgSpec(['a', 'b', 'c'], 'args', 'kwargs',
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(2, 3), ['size'], {'size': None}, {}))
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def test_mapwrapper_serial():
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in_arg = np.arange(10.)
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out_arg = np.sin(in_arg)
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p = MapWrapper(1)
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assert_(p._mapfunc is map)
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assert_(p.pool is None)
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assert_(p._own_pool is False)
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out = list(p(np.sin, in_arg))
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assert_equal(out, out_arg)
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with assert_raises(RuntimeError):
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p = MapWrapper(0)
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def test_pool():
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with Pool(2) as p:
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p.map(math.sin, [1, 2, 3, 4])
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def test_mapwrapper_parallel():
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in_arg = np.arange(10.)
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out_arg = np.sin(in_arg)
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with MapWrapper(2) as p:
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out = p(np.sin, in_arg)
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assert_equal(list(out), out_arg)
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assert_(p._own_pool is True)
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assert_(isinstance(p.pool, PWL))
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assert_(p._mapfunc is not None)
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# the context manager should've closed the internal pool
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# check that it has by asking it to calculate again.
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with assert_raises(Exception) as excinfo:
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p(np.sin, in_arg)
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assert_(excinfo.type is ValueError)
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# can also set a PoolWrapper up with a map-like callable instance
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with Pool(2) as p:
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q = MapWrapper(p.map)
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assert_(q._own_pool is False)
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q.close()
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# closing the PoolWrapper shouldn't close the internal pool
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# because it didn't create it
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out = p.map(np.sin, in_arg)
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assert_equal(list(out), out_arg)
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@_workers_wrapper
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def user_of_workers(x, b=1, workers=None):
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assert workers is not None
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assert isinstance(workers, MapWrapper)
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return np.array(list(workers(np.sin, x * b)))
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def test__workers_wrapper():
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arr = np.linspace(0, np.pi)
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req = np.sin(arr * 2.0)
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with Pool(2) as p:
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v = user_of_workers(arr, workers=p.map, b=2)
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assert_equal(v, req)
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v = user_of_workers(arr, workers=None, b=2)
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assert_equal(v, req)
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v = user_of_workers(arr, workers=2, b=2)
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assert_equal(v, req)
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# assess if decorator works with partial functions
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part_f = functools.partial(user_of_workers, b=2)
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assert_equal(part_f(arr), req)
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with Pool(2) as p:
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part_f = functools.partial(user_of_workers, b=2, workers=p.map)
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assert_equal(part_f(arr), req)
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def test_rng_integers():
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rng = np.random.RandomState()
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# test that numbers are inclusive of high point
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arr = rng_integers(rng, low=2, high=5, size=100, endpoint=True)
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assert np.max(arr) == 5
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assert np.min(arr) == 2
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assert arr.shape == (100, )
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# test that numbers are inclusive of high point
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arr = rng_integers(rng, low=5, size=100, endpoint=True)
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assert np.max(arr) == 5
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assert np.min(arr) == 0
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assert arr.shape == (100, )
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# test that numbers are exclusive of high point
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arr = rng_integers(rng, low=2, high=5, size=100, endpoint=False)
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assert np.max(arr) == 4
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assert np.min(arr) == 2
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assert arr.shape == (100, )
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# test that numbers are exclusive of high point
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arr = rng_integers(rng, low=5, size=100, endpoint=False)
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assert np.max(arr) == 4
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assert np.min(arr) == 0
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assert arr.shape == (100, )
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# now try with np.random.Generator
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try:
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rng = np.random.default_rng()
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except AttributeError:
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return
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# test that numbers are inclusive of high point
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arr = rng_integers(rng, low=2, high=5, size=100, endpoint=True)
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assert np.max(arr) == 5
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assert np.min(arr) == 2
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assert arr.shape == (100, )
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# test that numbers are inclusive of high point
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arr = rng_integers(rng, low=5, size=100, endpoint=True)
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assert np.max(arr) == 5
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assert np.min(arr) == 0
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assert arr.shape == (100, )
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# test that numbers are exclusive of high point
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arr = rng_integers(rng, low=2, high=5, size=100, endpoint=False)
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assert np.max(arr) == 4
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assert np.min(arr) == 2
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assert arr.shape == (100, )
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# test that numbers are exclusive of high point
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arr = rng_integers(rng, low=5, size=100, endpoint=False)
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assert np.max(arr) == 4
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assert np.min(arr) == 0
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assert arr.shape == (100, )
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class TestValidateInt:
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@pytest.mark.parametrize('n', [4, np.uint8(4), np.int16(4), np.array(4)])
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def test_validate_int(self, n):
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n = _validate_int(n, 'n')
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assert n == 4
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@pytest.mark.parametrize('n', [4.0, np.array([4]), Fraction(4, 1)])
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def test_validate_int_bad(self, n):
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with pytest.raises(TypeError, match='n must be an integer'):
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_validate_int(n, 'n')
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def test_validate_int_below_min(self):
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with pytest.raises(ValueError, match='n must be an integer not '
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'less than 0'):
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_validate_int(-1, 'n', 0)
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class TestRenameParameter:
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# check that wrapper `_rename_parameter` for backward-compatible
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# keyword renaming works correctly
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# Example method/function that still accepts keyword `old`
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@_rename_parameter("old", "new")
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def old_keyword_still_accepted(self, new):
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return new
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# Example method/function for which keyword `old` is deprecated
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@_rename_parameter("old", "new", dep_version="1.9.0")
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def old_keyword_deprecated(self, new):
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return new
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def test_old_keyword_still_accepted(self):
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# positional argument and both keyword work identically
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res1 = self.old_keyword_still_accepted(10)
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res2 = self.old_keyword_still_accepted(new=10)
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res3 = self.old_keyword_still_accepted(old=10)
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assert res1 == res2 == res3 == 10
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# unexpected keyword raises an error
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message = re.escape("old_keyword_still_accepted() got an unexpected")
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with pytest.raises(TypeError, match=message):
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self.old_keyword_still_accepted(unexpected=10)
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# multiple values for the same parameter raises an error
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message = re.escape("old_keyword_still_accepted() got multiple")
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with pytest.raises(TypeError, match=message):
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self.old_keyword_still_accepted(10, new=10)
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with pytest.raises(TypeError, match=message):
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self.old_keyword_still_accepted(10, old=10)
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with pytest.raises(TypeError, match=message):
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self.old_keyword_still_accepted(new=10, old=10)
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@pytest.fixture
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def kwarg_lock(self):
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from threading import Lock
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return Lock()
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def test_old_keyword_deprecated(self, kwarg_lock):
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# positional argument and both keyword work identically,
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# but use of old keyword results in DeprecationWarning
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dep_msg = "Use of keyword argument `old` is deprecated"
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res1 = self.old_keyword_deprecated(10)
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res2 = self.old_keyword_deprecated(new=10)
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# pytest warning filter is not thread-safe, enforce serialization
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with kwarg_lock:
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with pytest.warns(DeprecationWarning, match=dep_msg):
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res3 = self.old_keyword_deprecated(old=10)
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assert res1 == res2 == res3 == 10
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# unexpected keyword raises an error
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message = re.escape("old_keyword_deprecated() got an unexpected")
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with pytest.raises(TypeError, match=message):
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self.old_keyword_deprecated(unexpected=10)
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# multiple values for the same parameter raises an error and,
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# if old keyword is used, results in DeprecationWarning
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message = re.escape("old_keyword_deprecated() got multiple")
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with pytest.raises(TypeError, match=message):
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self.old_keyword_deprecated(10, new=10)
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with kwarg_lock:
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with pytest.raises(TypeError, match=message), \
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pytest.warns(DeprecationWarning, match=dep_msg):
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# breakpoint()
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self.old_keyword_deprecated(10, old=10)
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with kwarg_lock:
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with pytest.raises(TypeError, match=message), \
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pytest.warns(DeprecationWarning, match=dep_msg):
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self.old_keyword_deprecated(new=10, old=10)
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class TestContainsNaN:
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def test_policy(self):
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data = np.array([1, 2, 3, np.nan])
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assert _contains_nan(data) # default policy is "propagate"
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assert _contains_nan(data, nan_policy="propagate")
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assert _contains_nan(data, nan_policy="omit")
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assert not _contains_nan(data[:3])
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assert not _contains_nan(data[:3], nan_policy="propagate")
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assert not _contains_nan(data[:3], nan_policy="omit")
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with pytest.raises(ValueError, match="The input contains nan values"):
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_contains_nan(data, nan_policy="raise")
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assert not _contains_nan(data[:3], nan_policy="raise")
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with pytest.raises(ValueError, match="nan_policy must be one of"):
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_contains_nan(data, nan_policy="nan")
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def test_contains_nan(self):
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# Special case: empty array
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assert not _contains_nan(np.array([], dtype=float))
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# Integer arrays cannot contain NaN
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assert not _contains_nan(np.array([1, 2, 3]))
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assert not _contains_nan(np.array([[1, 2], [3, 4]]))
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assert not _contains_nan(np.array([1., 2., 3.]))
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assert not _contains_nan(np.array([1., 2.j, 3.]))
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assert _contains_nan(np.array([1., 2.j, np.nan]))
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assert _contains_nan(np.array([1., 2., np.nan]))
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assert _contains_nan(np.array([np.nan, 2., np.nan]))
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assert not _contains_nan(np.array([[1., 2.], [3., 4.]]))
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assert _contains_nan(np.array([[1., 2.], [3., np.nan]]))
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@skip_xp_invalid_arg
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def test_contains_nan_with_strings(self):
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data1 = np.array([1, 2, "3", np.nan]) # converted to string "nan"
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assert not _contains_nan(data1)
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data2 = np.array([1, 2, "3", np.nan], dtype='object')
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assert _contains_nan(data2)
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data3 = np.array([["1", 2], [3, np.nan]]) # converted to string "nan"
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assert not _contains_nan(data3)
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data4 = np.array([["1", 2], [3, np.nan]], dtype='object')
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assert _contains_nan(data4)
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@pytest.mark.skip_xp_backends(eager_only=True,
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reason="lazy backends tested separately")
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@pytest.mark.parametrize("nan_policy", ['propagate', 'omit', 'raise'])
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def test_array_api(self, xp, nan_policy):
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rng = np.random.default_rng(932347235892482)
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x0 = rng.random(size=(2, 3, 4))
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x = xp.asarray(x0)
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assert not _contains_nan(x, nan_policy)
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x = xpx.at(x)[1, 2, 1].set(xp.nan)
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if nan_policy == 'raise':
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with pytest.raises(ValueError, match="The input contains nan values"):
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_contains_nan(x, nan_policy)
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elif nan_policy == 'omit':
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assert _contains_nan(x, nan_policy, xp_omit_okay=True)
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elif nan_policy == 'propagate':
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assert _contains_nan(x, nan_policy)
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@pytest.mark.skip_xp_backends("numpy", reason="lazy backends only")
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@pytest.mark.skip_xp_backends("cupy", reason="lazy backends only")
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@pytest.mark.skip_xp_backends("array_api_strict", reason="lazy backends only")
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@pytest.mark.skip_xp_backends("torch", reason="lazy backends only")
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def test_array_api_lazy(self, xp):
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rng = np.random.default_rng(932347235892482)
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x0 = rng.random(size=(2, 3, 4))
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x = xp.asarray(x0)
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xp_assert_equal(_contains_nan(x), xp.asarray(False))
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xp_assert_equal(_contains_nan(x, "propagate"), xp.asarray(False))
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xp_assert_equal(_contains_nan(x, "omit", xp_omit_okay=True), xp.asarray(False))
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# Lazy arrays don't support "omit" and "raise" policies
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match = "not supported for lazy arrays"
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with pytest.raises(TypeError, match=match):
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_contains_nan(x, "omit")
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with pytest.raises(TypeError, match=match):
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_contains_nan(x, "raise")
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x = xpx.at(x)[1, 2, 1].set(np.nan)
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xp_assert_equal(_contains_nan(x), xp.asarray(True))
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xp_assert_equal(_contains_nan(x, "propagate"), xp.asarray(True))
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xp_assert_equal(_contains_nan(x, "omit", xp_omit_okay=True), xp.asarray(True))
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with pytest.raises(TypeError, match=match):
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_contains_nan(x, "omit")
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with pytest.raises(TypeError, match=match):
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_contains_nan(x, "raise")
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def test__rng_html_rewrite():
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def mock_str():
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lines = [
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'np.random.default_rng(8989843)',
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'np.random.default_rng(seed)',
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'np.random.default_rng(0x9a71b21474694f919882289dc1559ca)',
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' bob ',
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]
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return lines
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res = _rng_html_rewrite(mock_str)()
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ref = [
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'np.random.default_rng()',
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'np.random.default_rng(seed)',
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'np.random.default_rng()',
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' bob ',
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]
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assert res == ref
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class TestTransitionToRNG:
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def kmeans(self, **kwargs):
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rng = np.random.default_rng(3458934594269824562)
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return cluster.vq.kmeans2(rng.random(size=(20, 3)), 3, **kwargs)
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def kmeans2(self, **kwargs):
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rng = np.random.default_rng(3458934594269824562)
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return cluster.vq.kmeans2(rng.random(size=(20, 3)), 3, **kwargs)
|
|
|
|
def barycentric(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
x1, x2, y1 = rng.random((3, 10))
|
|
f = interpolate.BarycentricInterpolator(x1, y1, **kwargs)
|
|
return f(x2)
|
|
|
|
def clarkson_woodruff_transform(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
return linalg.clarkson_woodruff_transform(rng.random((10, 10)), 3, **kwargs)
|
|
|
|
def basinhopping(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
return optimize.basinhopping(optimize.rosen, rng.random(3), **kwargs).x
|
|
|
|
def opt(self, fun, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
bounds = optimize.Bounds(-rng.random(3) * 10, rng.random(3) * 10)
|
|
return fun(optimize.rosen, bounds, **kwargs).x
|
|
|
|
def differential_evolution(self, **kwargs):
|
|
return self.opt(optimize.differential_evolution, **kwargs)
|
|
|
|
def dual_annealing(self, **kwargs):
|
|
return self.opt(optimize.dual_annealing, **kwargs)
|
|
|
|
def check_grad(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
x = rng.random(3)
|
|
return optimize.check_grad(optimize.rosen, optimize.rosen_der, x,
|
|
direction='random', **kwargs)
|
|
|
|
def random_array(self, **kwargs):
|
|
return sparse.random_array((10, 10), density=1.0, **kwargs).toarray()
|
|
|
|
def random(self, **kwargs):
|
|
return sparse.random(10, 10, density=1.0, **kwargs).toarray()
|
|
|
|
def rand(self, **kwargs):
|
|
return sparse.rand(10, 10, density=1.0, **kwargs).toarray()
|
|
|
|
def svds(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
A = rng.random((10, 10))
|
|
return sparse.linalg.svds(A, **kwargs)
|
|
|
|
def random_rotation(self, **kwargs):
|
|
return spatial.transform.Rotation.random(3, **kwargs).as_matrix()
|
|
|
|
def goodness_of_fit(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
data = rng.random(100)
|
|
return stats.goodness_of_fit(stats.laplace, data, **kwargs).pvalue
|
|
|
|
def permutation_test(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
data = tuple(rng.random((2, 100)))
|
|
def statistic(x, y, axis): return np.mean(x, axis=axis) - np.mean(y, axis=axis)
|
|
return stats.permutation_test(data, statistic, **kwargs).pvalue
|
|
|
|
def bootstrap(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
data = (rng.random(100),)
|
|
return stats.bootstrap(data, np.mean, **kwargs).confidence_interval
|
|
|
|
def dunnett(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
x, y, control = rng.random((3, 100))
|
|
return stats.dunnett(x, y, control=control, **kwargs).pvalue
|
|
|
|
def sobol_indices(self, **kwargs):
|
|
def f_ishigami(x): return (np.sin(x[0]) + 7 * np.sin(x[1]) ** 2
|
|
+ 0.1 * (x[2] ** 4) * np.sin(x[0]))
|
|
dists = [stats.uniform(loc=-np.pi, scale=2 * np.pi),
|
|
stats.uniform(loc=-np.pi, scale=2 * np.pi),
|
|
stats.uniform(loc=-np.pi, scale=2 * np.pi)]
|
|
res = stats.sobol_indices(func=f_ishigami, n=1024, dists=dists, **kwargs)
|
|
return res.first_order
|
|
|
|
def qmc_engine(self, engine, **kwargs):
|
|
qrng = engine(d=1, **kwargs)
|
|
return qrng.random(4)
|
|
|
|
def halton(self, **kwargs):
|
|
return self.qmc_engine(stats.qmc.Halton, **kwargs)
|
|
|
|
def sobol(self, **kwargs):
|
|
return self.qmc_engine(stats.qmc.Sobol, **kwargs)
|
|
|
|
def latin_hypercube(self, **kwargs):
|
|
return self.qmc_engine(stats.qmc.LatinHypercube, **kwargs)
|
|
|
|
def poisson_disk(self, **kwargs):
|
|
return self.qmc_engine(stats.qmc.PoissonDisk, **kwargs)
|
|
|
|
def multivariate_normal_qmc(self, **kwargs):
|
|
X = stats.qmc.MultivariateNormalQMC([0], **kwargs)
|
|
return X.random(4)
|
|
|
|
def multinomial_qmc(self, **kwargs):
|
|
X = stats.qmc.MultinomialQMC([0.5, 0.5], 4, **kwargs)
|
|
return X.random(4)
|
|
|
|
def permutation_method(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
data = tuple(rng.random((2, 100)))
|
|
method = stats.PermutationMethod(**kwargs)
|
|
return stats.pearsonr(*data, method=method).pvalue
|
|
|
|
def bootstrap_method(self, **kwargs):
|
|
rng = np.random.default_rng(3458934594269824562)
|
|
data = tuple(rng.random((2, 100)))
|
|
res = stats.pearsonr(*data)
|
|
method = stats.BootstrapMethod(**kwargs)
|
|
return res.confidence_interval(method=method)
|
|
|
|
@pytest.mark.fail_slow(10)
|
|
@pytest.mark.slow
|
|
@pytest.mark.parametrize("method, arg_name", [
|
|
(kmeans, "seed"),
|
|
(kmeans2, "seed"),
|
|
(barycentric, "random_state"),
|
|
(clarkson_woodruff_transform, "seed"),
|
|
(basinhopping, "seed"),
|
|
(differential_evolution, "seed"),
|
|
(dual_annealing, "seed"),
|
|
(check_grad, "seed"),
|
|
(random_array, 'random_state'),
|
|
(random, 'random_state'),
|
|
(rand, 'random_state'),
|
|
(random_rotation, "random_state"),
|
|
(goodness_of_fit, "random_state"),
|
|
(permutation_test, "random_state"),
|
|
(bootstrap, "random_state"),
|
|
(permutation_method, "random_state"),
|
|
(bootstrap_method, "random_state"),
|
|
(dunnett, "random_state"),
|
|
(sobol_indices, "random_state"),
|
|
(halton, "seed"),
|
|
(sobol, "seed"),
|
|
(latin_hypercube, "seed"),
|
|
(poisson_disk, "seed"),
|
|
(multivariate_normal_qmc, "seed"),
|
|
(multinomial_qmc, "seed"),
|
|
])
|
|
def test_rng_deterministic(self, method, arg_name):
|
|
np.random.seed(None)
|
|
seed = 2949672964
|
|
|
|
rng = np.random.default_rng(seed)
|
|
message = "got multiple values for argument now known as `rng`"
|
|
with pytest.raises(TypeError, match=message):
|
|
method(self, **{'rng': rng, arg_name: seed})
|
|
|
|
rng = np.random.default_rng(seed)
|
|
res1 = method(self, rng=rng)
|
|
res2 = method(self, rng=seed)
|
|
assert_equal(res2, res1)
|
|
|
|
if method.__name__ in {"dunnett", "sobol_indices"}:
|
|
# the two kwargs have essentially the same behavior for these functions
|
|
res3 = method(self, **{arg_name: seed})
|
|
assert_equal(res3, res1)
|
|
return
|
|
|
|
rng = np.random.RandomState(seed)
|
|
res1 = method(self, **{arg_name: rng})
|
|
res2 = method(self, **{arg_name: seed})
|
|
|
|
if method.__name__ in {"halton", "sobol", "latin_hypercube", "poisson_disk",
|
|
"multivariate_normal_qmc", "multinomial_qmc"}:
|
|
# For these, passing `random_state=RandomState(seed)` is not the same as
|
|
# passing integer `seed`.
|
|
res1b = method(self, **{arg_name: np.random.RandomState(seed)})
|
|
assert_equal(res1b, res1)
|
|
res2b = method(self, **{arg_name: seed})
|
|
assert_equal(res2b, res2)
|
|
return
|
|
|
|
np.random.seed(seed)
|
|
res3 = method(self, **{arg_name: None})
|
|
assert_equal(res2, res1)
|
|
assert_equal(res3, res1)
|