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from iminuit import util
import pytest
from argparse import Namespace
from numpy.testing import assert_equal, assert_allclose
import numpy as np
from iminuit._core import MnUserParameterState
from iminuit._optional_dependencies import optional_module_for
import pickle
from iminuit._hide_modules import hide_modules
try:
import scipy # noqa
scipy_available = True
except ModuleNotFoundError:
scipy_available = False
def test_ndim():
ndim = util._ndim
assert ndim(1) == 0
assert ndim([]) == 1
assert ndim([[]]) == 2
assert ndim(None) == 0
assert ndim((None, None)) == 1
assert ndim(((1, 2), None)) == 2
assert ndim((None, (1, 2))) == 2
def test_BasicView():
with pytest.raises(TypeError):
util.BasicView(None, 2)
def test_ValueView():
state = MnUserParameterState()
state.add("x", 1.0, 0.1)
state.add("y", 2.2, 0.1)
state.add("z", 3.3, 0.1)
v = util.ValueView(
Namespace(
_var2pos={"x": 0, "y": 1, "z": 2},
_pos2var=("x", "y", "z"),
npar=3,
_last_state=state,
_copy_state_if_needed=lambda: None,
)
)
assert v == v
assert v == (1.0, 2.2, 3.3)
assert v != (1.0, 2.1, 3.3)
assert v != 0
assert repr(v) == "<ValueView x=1.0 y=2.2 z=3.3>"
assert str(v) == repr(v)
v[:] = (1, 2, 3)
assert_equal(v[:3], (1, 2, 3))
assert_equal(v[0:3], (1, 2, 3))
assert_equal(v[0:10], (1, 2, 3))
assert_equal(v, (1, 2, 3))
v[1:] = 4
assert_equal(v, (1, 4, 4))
v["y"] = 2
assert_equal(v, (1, 2, 4))
v["y":] = 3
assert_equal(v, (1, 3, 3))
v[:"z"] = 2
assert_equal(v, (2, 2, 3))
v_dict = v.to_dict()
assert isinstance(v_dict, dict)
assert v_dict["x"] == v["x"]
assert v_dict["y"] == v["y"]
assert v_dict["z"] == v["z"]
v[:] = (1, 2, 3)
assert_equal(v[["x", "z"]], (1, 3))
assert_equal(v[[2, 0]], (3, 1))
v[["x", "z"]] = (3, 1)
assert_equal(v, (3, 2, 1))
def test_FixedView_as_mask_for_other_views():
state = MnUserParameterState()
state.add("x", 1, 0.1)
state.add("y", 2, 0.1)
state.add("z", 3, 0.1)
fake_minuit = Namespace(
_var2pos={"x": 0, "y": 1, "z": 2},
_pos2var=("x", "y", "z"),
npar=3,
_last_state=state,
_copy_state_if_needed=lambda: None,
)
v = util.ValueView(fake_minuit)
f = util.FixedView(fake_minuit)
f[1] = True
assert_equal(f, [False, True, False])
assert_equal(v[f], [2])
assert_equal(v[~f], [1, 3])
v[f] = 5
assert_equal(v, [1, 5, 3])
v[~f] = [2, 4]
assert_equal(v, [2, 5, 4])
def test_FixedView_comparison_with_broadcasting():
state = MnUserParameterState()
state.add("x", 1, 0.1)
state.add("y", 2, 0.1)
state.add("z", 3, 0.1)
fake_minuit = Namespace(
_var2pos={"x": 0, "y": 1, "z": 2},
_pos2var=("x", "y", "z"),
npar=3,
_last_state=state,
_copy_state_if_needed=lambda: None,
)
f = util.FixedView(fake_minuit)
assert_equal(f, [False, False, False])
# broadcasting
assert f == False # noqa
f[0] = True
assert_equal(f, [True, False, False])
assert f != False # noqa
def test_Matrix():
m = util.Matrix(("a", "b"))
m[:] = [[1, 2], [2, 8]]
assert_equal(m, ((1, 2), (2, 8)))
assert repr(m) == "[[1. 2.]\n [2. 8.]]"
c = m.correlation()
assert_allclose(c, ((1.0, 0.5**0.5), (0.5**0.5, 1.0)))
assert m["a", "b"] == 2.0
assert m["a", 1] == 2.0
assert m[1, "a"] == 2.0
assert m[1, 1] == 8.0
assert_equal(m[0], [1, 2])
assert_equal(m["b"], (2, 8))
assert_equal(m[:], [[1, 2], [2, 8]])
assert_equal(m[:, 0], [1, 2])
assert_equal(m[:, 1], [2, 8])
# this swaps rows and cols
assert_equal(m[[1, 0]], [[8, 2], [2, 1]])
m *= 2
assert_equal(m, ((2, 4), (4, 16)))
m2 = np.dot(m, (1, 1))
assert repr(m2) == "[ 6. 20.]"
assert str(m2) == "[ 6. 20.]"
assert_allclose(m2, (6, 20))
# matrix is always square
m = util.Matrix(("a", "b", "c"))
m[:] = np.arange(9).reshape((3, 3))
# [0 1 2
# 3 4 5
# 6 7 8]
# m1 = m[:2]
# assert_equal(m1, [[0, 1], [3, 4]])
m2 = m[[0, 2]]
assert_equal(m2, [[0, 2], [6, 8]])
m3 = m[["a", "c"]]
assert_equal(m3, [[0, 2], [6, 8]])
d = m.to_dict()
assert list(d.keys()) == [
("a", "a"),
("a", "b"),
("a", "c"),
("b", "b"),
("b", "c"),
("c", "c"),
]
for k, v in d.items():
assert v == m[k]
with pytest.raises(TypeError):
util.Matrix("ab")
with pytest.raises(TypeError):
util.Matrix(1)
m2 = pickle.loads(pickle.dumps(m))
assert type(m2) is util.Matrix
assert_equal(m2, m)
assert m2._var2pos == m._var2pos
def test_Param():
values = 3, "foo", 1.2, 3.4, None, False, False, 42, None
p = util.Param(*values)
assert p.number == 3
assert p.name == "foo"
assert p.value == 1.2
assert p.error == 3.4
assert p.merror is None
assert not p.is_const
assert not p.is_fixed
assert p.has_limits
assert p.has_lower_limit
assert not p.has_upper_limit
assert p.lower_limit == 42
assert p.upper_limit is None
assert repr(p) == (
"Param(number=3, name='foo', value=1.2, error=3.4, merror=None, "
"is_const=False, is_fixed=False, lower_limit=42, upper_limit=None)"
)
def test_Params():
p = util.Params(
[
util.Param(0, "foo", 1.2, 3.4, None, False, False, 42, None),
util.Param(1, "bar", 3.4, 4.5, None, False, False, 42, None),
]
)
assert repr(p) == repr((p[0], p[1]))
assert p[0].number == 0
assert p[1].number == 1
assert p["foo"].number == 0
assert p["bar"].number == 1
def test_MError():
me = util.MError(
1,
"x",
0.1,
0.2,
True,
True,
True,
False,
False,
False,
False,
False,
False,
11,
0.7,
)
assert repr(me) == (
"<MError number=1 name='x' lower=0.1 upper=0.2 is_valid=True lower_valid=True "
"upper_valid=True at_lower_limit=False at_upper_limit=False "
"at_lower_max_fcn=False at_upper_max_fcn=False lower_new_min=False "
"upper_new_min=False nfcn=11 min=0.7>"
)
assert me == util.MError(
1,
"x",
0.1,
0.2,
True,
True,
True,
False,
False,
False,
False,
False,
False,
11,
0.7,
)
assert me != util.MError(
1,
"x",
0.1,
0.2,
True,
True,
True,
False,
False,
False,
False,
False,
False,
11,
0.8,
)
def test_MErrors():
mes = util.MErrors(
x=util.MError(
1,
"x",
0.1,
0.2,
True,
True,
True,
False,
False,
False,
False,
False,
False,
11,
0.7,
)
)
assert repr(mes) == f"<MErrors\n {mes['x']!r}\n>"
@pytest.mark.parametrize("errordef", (0.5, 1.0))
def test_FMin(errordef):
fm = Namespace(
fval=1.23456e-10,
edm=1.23456e-10,
errordef=errordef,
is_valid=True,
has_valid_parameters=True,
has_accurate_covar=True,
has_posdef_covar=True,
has_made_posdef_covar=False,
hesse_failed=False,
has_covariance=True,
is_above_max_edm=False,
has_reached_call_limit=False,
has_parameters_at_limit=False,
state=[],
)
fmin = util.FMin(fm, "foo", 1, 2, 1, 0.1, 1.2)
assert {x for x in dir(fmin) if not x.startswith("_")} == {
"algorithm",
"edm",
"edm_goal",
"errordef",
"fval",
"reduced_chi2",
"nfcn",
"ngrad",
"is_valid",
"has_accurate_covar",
"has_valid_parameters",
"has_posdef_covar",
"has_made_posdef_covar",
"hesse_failed",
"has_covariance",
"is_above_max_edm",
"has_reached_call_limit",
"has_parameters_at_limit",
"time",
}
assert fmin.algorithm == "foo"
assert fmin.edm == 1.23456e-10
assert fmin.edm_goal == 0.1
assert not fmin.has_parameters_at_limit
assert fmin.time == 1.2
assert fmin == util.FMin(fm, "foo", 1, 2, 1, 0.1, 1.2)
assert fmin != util.FMin(fm, "foo", 1, 2, 1, 0.3, 1.2)
assert fmin != util.FMin(fm, "bar", 1, 2, 1, 0.1, 1.2)
assert fmin != util.FMin(fm, "foo", 1, 2, 1, 0.1, 1.5)
if errordef == 1:
reduced_chi2 = fmin.fval
else:
reduced_chi2 = np.nan
assert repr(fmin) == (
f"<FMin algorithm='foo' edm=1.23456e-10 edm_goal=0.1 errordef={errordef}"
" fval=1.23456e-10"
" has_accurate_covar=True has_covariance=True has_made_posdef_covar=False"
" has_parameters_at_limit=False has_posdef_covar=True"
" has_reached_call_limit=False has_valid_parameters=True"
" hesse_failed=False is_above_max_edm=False is_valid=True"
f" nfcn=1 ngrad=2 reduced_chi2={reduced_chi2} time=1.2>"
)
def test_normalize_limit():
assert util._normalize_limit(None) == (-np.inf, np.inf)
assert util._normalize_limit((None, 2)) == (-np.inf, 2)
assert util._normalize_limit((2, None)) == (2, np.inf)
assert util._normalize_limit((None, None)) == (-np.inf, np.inf)
with pytest.raises(ValueError):
util._normalize_limit((3, 2))
def test_guess_initial_step():
assert util._guess_initial_step(0) == 0.1
assert util._guess_initial_step(1) == 0.01
def test_address_of_cfunc():
nb = pytest.importorskip("numba")
nb_sig = nb.types.double(nb.types.uintc, nb.types.CPointer(nb.types.double))
@nb.cfunc(nb_sig)
def fcn(n, x):
x = nb.carray(x, (n,))
r = 0.0
for i in range(n):
r += (x[i] - i) ** 2
return r
from ctypes import cast, c_void_p, CFUNCTYPE, POINTER, c_double, c_uint32
address = cast(fcn.ctypes, c_void_p).value
assert util._address_of_cfunc(fcn) == address
# let's see if we can call the function pointer, going full circle
c_sig = CFUNCTYPE(c_double, c_uint32, POINTER(c_double))
c_fcn = cast(address, c_sig)
v = np.array((1.0, 2.0))
assert c_fcn(2, v.ctypes.data_as(POINTER(c_double))) == 2.0
def test_address_of_cfunc_bad_signature():
nb = pytest.importorskip("numba")
nb_sig = nb.types.double(nb.types.double, nb.types.CPointer(nb.types.double))
@nb.cfunc(nb_sig)
def fcn(y, x):
return 0
assert util._address_of_cfunc(fcn) == 0
def test_make_func_code():
with pytest.warns(FutureWarning):
fc = util.make_func_code(["a", "b"])
assert fc.co_varnames == ("a", "b")
assert fc.co_argcount == 2
with pytest.warns(FutureWarning):
fc = util.make_func_code(("x",))
assert fc.co_varnames == ("x",)
assert fc.co_argcount == 1
def test_make_with_signature():
def f(a, b):
return a + b
f1 = util.make_with_signature(f, "x", "y")
assert util.describe(f1) == ["x", "y"]
assert f1(1, 2) == f(1, 2)
f2 = util.make_with_signature(f, b="z")
assert util.describe(f2) == ["a", "z"]
assert f2(1, 2) == f(1, 2)
assert f1 is not f2
f3 = util.make_with_signature(f, "x", b="z")
assert util.describe(f3) == ["x", "z"]
assert f3(1, 2) == f(1, 2)
# check that arguments are not overridden
assert util.describe(f1) == ["x", "y"]
assert util.describe(f) == ["a", "b"]
with pytest.raises(ValueError):
util.make_with_signature(f, "a", "b", "c")
with pytest.raises(ValueError):
util.make_with_signature(f, "a", "b", "c", b="z")
def test_make_with_signature_on_func_without_code_object():
class Fcn:
def __call__(self, x, y):
return x + y
f = Fcn()
assert not hasattr(f, "__code__")
f1 = util.make_with_signature(f, "x", "y")
assert util.describe(f1) == ["x", "y"]
assert f1(1, 2) == f(1, 2)
assert f1 is not f
f2 = util.make_with_signature(f1, x="a")
assert util.describe(f2) == ["a", "y"]
assert f2(1, 2) == f(1, 2)
def test_merge_signatures():
def f(x, y, z):
return x + y + z
def g(x, a, b):
return x + a + b
args, (pf, pg) = util.merge_signatures([f, g])
assert args == ["x", "y", "z", "a", "b"]
assert pf == [0, 1, 2]
assert pg == [0, 3, 4]
@pytest.mark.skipif(not scipy_available, reason="needs scipy")
def test_propagate_1():
cov = [
[1.0, 0.1, 0.2],
[0.1, 2.0, 0.3],
[0.2, 0.3, 3.0],
]
x = [1, 2, 3]
def fn(x):
return 2 * x + 1
with pytest.warns(FutureWarning):
y, ycov = util.propagate(fn, x, cov)
np.testing.assert_allclose(y, [3, 5, 7])
np.testing.assert_allclose(
ycov, [[4, 0.4, 0.8], [0.4, 8, 1.2], [0.8, 1.2, 12]], rtol=1e-3
)
with pytest.warns(FutureWarning):
y, ycov = util.propagate(fn, [1], [[2]])
np.testing.assert_allclose(y, 3)
np.testing.assert_allclose(ycov, 8, rtol=1e-3)
@pytest.mark.skipif(not scipy_available, reason="needs scipy")
def test_propagate_2():
cov = [
[1.0, 0.1, 0.2],
[0.1, 2.0, 0.3],
[0.2, 0.3, 3.0],
]
x = [1.0, 2.0, 3.0]
a = 0.5 * np.arange(30).reshape((10, 3))
def fn(x):
return np.dot(a, x)
with pytest.warns(FutureWarning):
y, ycov = util.propagate(fn, x, cov)
np.testing.assert_equal(y, fn(x))
np.testing.assert_allclose(ycov, np.einsum("ij,kl,jl", a, a, cov), rtol=1e-3)
def fn(x):
return np.linalg.multi_dot([x.T, cov, x])
with pytest.warns(FutureWarning):
y, ycov = util.propagate(fn, x, cov)
np.testing.assert_equal(y, fn(np.array(x)))
jac = 2 * np.dot(cov, x)
np.testing.assert_allclose(ycov, np.einsum("i,k,ik", jac, jac, cov), rtol=1e-3)
@pytest.mark.skipif(not scipy_available, reason="needs scipy")
def test_propagate_3():
# matrices with full zero rows and columns are supported
cov = [
[1.0, 0.0, 0.2],
[0.0, 0.0, 0.0],
[0.2, 0.0, 3.0],
]
x = [1.0, 2.0, 3.0]
def fn(x):
return 2 * x + 1
with pytest.warns(FutureWarning):
y, ycov = util.propagate(fn, x, cov)
np.testing.assert_allclose(y, [3, 5, 7])
np.testing.assert_allclose(ycov, [[4, 0.0, 0.8], [0.0, 0.0, 0.0], [0.8, 0.0, 12]])
@pytest.mark.skipif(not scipy_available, reason="needs scipy")
def test_propagate_on_bad_input():
cov = [[np.nan, 0.0], [0.0, 1.0]]
x = [1.0, 2.0]
def fn(x):
return 2 * x + 1
with pytest.warns(FutureWarning):
with pytest.raises(ValueError):
util.propagate(fn, x, cov)
with pytest.warns(FutureWarning):
with pytest.raises(ValueError):
util.propagate(fn, x, 1)
cov = [[1.0], [1.0]]
with pytest.warns(FutureWarning):
with pytest.raises(ValueError):
util.propagate(fn, x, cov)
def test_iterate():
assert list(util._iterate(1)) == [1]
assert list(util._iterate([1, 2])) == [1, 2]
def test_replace_none():
assert util._replace_none(None, 2) == 2
assert util._replace_none(3, 2) == 3
def test_progressbar(capsys):
with util.ProgressBar(max_value=4) as bar:
for i in range(4):
bar += 1
stdout, stderr = capsys.readouterr()
assert stdout == "\r0 %\r25 %\r50 %\r75 %\r100 %\r "
def test_progressbar_no_ipykernel(capsys):
with hide_modules("ipykernel"):
with util.ProgressBar(max_value=4) as bar:
for i in range(4):
bar += 1
stdout, stderr = capsys.readouterr()
assert stdout == "\r0 %\r25 %\r50 %\r75 %\r100 %\r "
def test_progressbar_html(capsys):
import sys
m_iostream = pytest.importorskip("ipykernel.iostream")
m_display = pytest.importorskip("IPython.display")
class OutStream:
def write(self, s):
original_stdout.write(s)
def flush(self):
original_stdout.flush()
def display(msg, **kwargs):
sys.stdout.write(msg._repr_html_())
original_stdout = sys.stdout
# make ProgressBar think it is running in Jupyter
sys.stdout = OutStream()
# monkey-patching our mockups
m_iostream.OutStream = OutStream
m_display.display = display
with util.ProgressBar(max_value=4) as bar:
for i in range(4):
bar += 1
sys.stdout = original_stdout
stdout, stderr = capsys.readouterr()
assert stdout == (
"<progress value='0' max='100'></progress> 0 %"
"<progress value='25' max='100'></progress> 25 %"
"<progress value='50' max='100'></progress> 50 %"
"<progress value='75' max='100'></progress> 75 %"
"<progress value='100' max='100'></progress> 100 %"
)
@pytest.mark.parametrize(
"mask_expected",
(
(None, [[0, 1, 2]]),
([True, False], [[0]]),
([False, True], [[1]]),
([True, True, True, False, True, True, False, True], [[0, 1, 2], [4, 5], [7]]),
),
)
def test_histogram_segments(mask_expected):
mask, expected = mask_expected
if mask is None:
xe = np.linspace(0, 1, 4)
masked = np.arange(3)
else:
xe = np.linspace(0, 1, len(mask))
masked = np.arange(len(mask))[np.array(mask)]
segments = util._histogram_segments(mask, xe, masked)
assert_equal([s[0] for s in segments], expected)
@pytest.mark.parametrize(
"fn_expected", ((lambda x: x, 40), (lambda x: x**11, 60), (np.log, 80))
)
def test_smart_sampling_1(fn_expected):
fn, expected = fn_expected
x, y = util._smart_sampling(fn, 1e-10, 5)
assert len(y) < expected
def test_smart_sampling_2():
# should not raise a warning
x, y = util._smart_sampling(np.log, 1e-10, 1, tol=1e-5)
assert 0 < len(x) < 1000
def test_smart_sampling_3():
def step(x):
return np.where(x > 0.5, 0, 1)
with pytest.warns(RuntimeWarning, match="Iteration limit"):
x, y = util._smart_sampling(step, 0, 1, tol=0)
assert 0 < len(x) < 80
def test_smart_sampling_4():
from time import sleep
def step(x):
sleep(0.1)
return np.where(x > 0.5, 0, 1)
with pytest.warns(RuntimeWarning, match="Time limit"):
x, y = util._smart_sampling(step, 0, 1, maxtime=0)
assert 0 < len(x) < 30
@pytest.mark.parametrize(
"x,expected",
[([1, 2, 3], False), ([-1, 1000, 100000], False), ([1, 10, 100], True)],
)
def test_detect_log_spacing_1(x, expected):
assert util._detect_log_spacing(x) == expected
def test_optional_module_for_1():
with optional_module_for("foo"):
import iminuit # noqa
def test_optional_module_for_2():
from iminuit.warnings import OptionalDependencyWarning
with pytest.warns(
OptionalDependencyWarning, match="foo requires optional package 'foobarbaz'"
):
with optional_module_for("foo"):
import foobarbaz # noqa
def test_optional_module_for_3():
from iminuit.warnings import OptionalDependencyWarning
with pytest.warns(
OptionalDependencyWarning, match="foo requires optional package 'foo'"
):
with optional_module_for("foo", replace={"foobarbaz": "foo"}):
import foobarbaz # noqa
def test_positive_definite():
assert util.is_positive_definite([[1, 0], [0, 1]])
assert not util.is_positive_definite([[1, 1], [1, 1]])
assert not util.is_positive_definite([[1, 0], [1, 1]])
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