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Mar 27, 2024
Merged

List more math function in API docs #7211

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9e8601c
This commit is a partial solution to the problems presented in PyMC g…
brandonhorsley Feb 29, 2024
a35a40e
Removed numpy functions and tround from math.rst
brandonhorsley Mar 25, 2024
a971005
Edits to math.py.
brandonhorsley Mar 25, 2024
0f43005
Update pymc/math.py
brandonhorsley Mar 25, 2024
efa4543
Update pymc/math.py
brandonhorsley Mar 25, 2024
8166fe0
Further FutureWarnings applied to _numpy functions
brandonhorsley Mar 25, 2024
4045bc2
Undid test_math edits, test_continuous change
brandonhorsley Mar 25, 2024
b14e000
Removed a FutureWarning I forgot to remove
brandonhorsley Mar 25, 2024
7f3eb36
refactor helper function
ricardoV94 Mar 25, 2024
43ec2ed
Tweak tests
ricardoV94 Mar 25, 2024
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1 change: 1 addition & 0 deletions tests/distributions/test_continuous.py
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Original file line number Diff line number Diff line change
Expand Up @@ -418,6 +418,7 @@ def scipy_log_pdf(value, a, b):
return np.log(a) + np.log(b) + (a - 1) * np.log(value) + (b - 1) * np.log(1 - value**a)

def scipy_log_cdf(value, a, b):
warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
return pm.math.log1mexp_numpy(b * np.log1p(-(value**a)), negative_input=True)

check_logp(
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12 changes: 9 additions & 3 deletions tests/test_math.py
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Expand Up @@ -29,10 +29,10 @@
kron_solve_lower,
kronecker,
log1mexp,
log1mexp_numpy,
log1mexp_numpy, # to be deprecated
logdet,
logdiffexp,
logdiffexp_numpy,
logdiffexp_numpy, # to be deprecated
probit,
)
from pymc.pytensorf import floatX
Expand Down Expand Up @@ -148,6 +148,8 @@ def test_log1mexp():
with warnings.catch_warnings():
warnings.filterwarnings("ignore", "divide by zero encountered in log", RuntimeWarning)
warnings.filterwarnings("ignore", "invalid value encountered in log", RuntimeWarning)

warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
actual_ = log1mexp_numpy(-vals, negative_input=True)
npt.assert_allclose(actual_, expected)
# Check that input was not changed in place
Expand All @@ -158,10 +160,12 @@ def test_log1mexp_numpy_no_warning():
"""Assert RuntimeWarning is not raised for very small numbers"""
with warnings.catch_warnings():
warnings.simplefilter("error")
warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
log1mexp_numpy(-1e-25, negative_input=True)


def test_log1mexp_numpy_integer_input():
warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
assert np.isclose(log1mexp_numpy(-2, negative_input=True), pt.log1mexp(-2).eval())


Expand All @@ -170,10 +174,12 @@ def test_log1mexp_deprecation_warnings():
FutureWarning,
match="pymc.math.log1mexp_numpy will expect a negative input",
):
warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
res_pos = log1mexp_numpy(2)

with warnings.catch_warnings():
warnings.simplefilter("error")
warnings.warn("pymc.math.log1mexp_numpy is being deprecated.", FutureWarning)
res_neg = log1mexp_numpy(-2, negative_input=True)

with pytest.warns(
Expand All @@ -196,7 +202,7 @@ def test_logdiffexp():
with warnings.catch_warnings():
warnings.filterwarnings("ignore", "divide by zero encountered in log", RuntimeWarning)
b = np.log([0, 1, 2, 3])

warnings.warn("pymc.math.logdiffexp_numpy is being deprecated.", FutureWarning)
assert np.allclose(logdiffexp_numpy(a, b), 0)
assert np.allclose(logdiffexp(a, b).eval(), 0)

Expand Down