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MarcoGorelliMarcoGorelli
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remove sd deprecation warning
1 parent e0ee447 commit 6169b5b

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5 files changed

+19
-40
lines changed

5 files changed

+19
-40
lines changed

‎pymc3/distributions/continuous.py

Lines changed: 10 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -478,9 +478,8 @@ class Normal(Continuous):
478478
def __init__(self, mu=0, sigma=None, tau=None, sd=None, **kwargs):
479479
if sd is not None:
480480
sigma = sd
481-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
482481
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
483-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
482+
self.sigma = tt.as_tensor_variable(sigma)
484483
self.tau = tt.as_tensor_variable(tau)
485484

486485
self.mean = self.median = self.mode = self.mu = mu = tt.as_tensor_variable(floatX(mu))
@@ -640,9 +639,8 @@ def __init__(
640639
):
641640
if sd is not None:
642641
sigma = sd
643-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
644642
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
645-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
643+
self.sigma = tt.as_tensor_variable(sigma)
646644
self.tau = tt.as_tensor_variable(tau)
647645
self.lower_check = tt.as_tensor_variable(floatX(lower)) if lower is not None else lower
648646
self.upper_check = tt.as_tensor_variable(floatX(upper)) if upper is not None else upper
@@ -835,11 +833,10 @@ class HalfNormal(PositiveContinuous):
835833
def __init__(self, sigma=None, tau=None, sd=None, *args, **kwargs):
836834
if sd is not None:
837835
sigma = sd
838-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
839836
super().__init__(*args, **kwargs)
840837
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
841838

842-
self.sigma = self.sd = sigma = tt.as_tensor_variable(sigma)
839+
self.sigma = sigma = tt.as_tensor_variable(sigma)
843840
self.tau = tau = tt.as_tensor_variable(tau)
844841

845842
self.mean = tt.sqrt(2 / (np.pi * self.tau))
@@ -1218,7 +1215,6 @@ def __init__(self, alpha=None, beta=None, mu=None, sigma=None, sd=None, *args, *
12181215
super().__init__(*args, **kwargs)
12191216
if sd is not None:
12201217
sigma = sd
1221-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
12221218
alpha, beta = self.get_alpha_beta(alpha, beta, mu, sigma)
12231219
self.alpha = alpha = tt.as_tensor_variable(floatX(alpha))
12241220
self.beta = beta = tt.as_tensor_variable(floatX(beta))
@@ -1724,13 +1720,12 @@ def __init__(self, mu=0, sigma=None, tau=None, sd=None, *args, **kwargs):
17241720
super().__init__(*args, **kwargs)
17251721
if sd is not None:
17261722
sigma = sd
1727-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
17281723

17291724
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
17301725

17311726
self.mu = mu = tt.as_tensor_variable(floatX(mu))
17321727
self.tau = tau = tt.as_tensor_variable(tau)
1733-
self.sigma = self.sd = sigma = tt.as_tensor_variable(sigma)
1728+
self.sigma = sigma = tt.as_tensor_variable(sigma)
17341729

17351730
self.mean = tt.exp(self.mu + 1.0 / (2 * self.tau))
17361731
self.median = tt.exp(self.mu)
@@ -1884,15 +1879,13 @@ class StudentT(Continuous):
18841879
"""
18851880

18861881
def __init__(self, nu, mu=0, lam=None, sigma=None, sd=None, *args, **kwargs):
1887-
super().__init__(*args, **kwargs)
18881882
super().__init__(*args, **kwargs)
18891883
if sd is not None:
18901884
sigma = sd
1891-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
18921885
self.nu = nu = tt.as_tensor_variable(floatX(nu))
18931886
lam, sigma = get_tau_sigma(tau=lam, sigma=sigma)
18941887
self.lam = lam = tt.as_tensor_variable(lam)
1895-
self.sigma = self.sd = sigma = tt.as_tensor_variable(sigma)
1888+
self.sigma = sigma = tt.as_tensor_variable(sigma)
18961889
self.mean = self.median = self.mode = self.mu = mu = tt.as_tensor_variable(mu)
18971890

18981891
self.variance = tt.switch((nu > 2) * 1, (1 / self.lam) * (nu / (nu - 2)), np.inf)
@@ -2397,7 +2390,6 @@ def __init__(self, alpha=None, beta=None, mu=None, sigma=None, sd=None, *args, *
23972390
super().__init__(*args, **kwargs)
23982391
if sd is not None:
23992392
sigma = sd
2400-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
24012393

24022394
alpha, beta = self.get_alpha_beta(alpha, beta, mu, sigma)
24032395
self.alpha = alpha = tt.as_tensor_variable(floatX(alpha))
@@ -2545,7 +2537,6 @@ def __init__(self, alpha=None, beta=None, mu=None, sigma=None, sd=None, *args, *
25452537

25462538
if sd is not None:
25472539
sigma = sd
2548-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
25492540

25502541
alpha, beta = InverseGamma._get_alpha_beta(alpha, beta, mu, sigma)
25512542
self.alpha = alpha = tt.as_tensor_variable(floatX(alpha))
@@ -2902,12 +2893,11 @@ def __init__(self, nu=1, sigma=None, lam=None, sd=None, *args, **kwargs):
29022893
super().__init__(*args, **kwargs)
29032894
if sd is not None:
29042895
sigma = sd
2905-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
29062896

29072897
self.mode = tt.as_tensor_variable(0)
29082898
lam, sigma = get_tau_sigma(lam, sigma)
29092899
self.median = tt.as_tensor_variable(sigma)
2910-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
2900+
self.sigma = tt.as_tensor_variable(sigma)
29112901
self.lam = tt.as_tensor_variable(lam)
29122902
self.nu = nu = tt.as_tensor_variable(floatX(nu))
29132903

@@ -3041,10 +3031,9 @@ def __init__(self, mu=0.0, sigma=None, nu=None, sd=None, *args, **kwargs):
30413031

30423032
if sd is not None:
30433033
sigma = sd
3044-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
30453034

30463035
self.mu = mu = tt.as_tensor_variable(floatX(mu))
3047-
self.sigma = self.sd = sigma = tt.as_tensor_variable(floatX(sigma))
3036+
self.sigma = sigma = tt.as_tensor_variable(floatX(sigma))
30483037
self.nu = nu = tt.as_tensor_variable(floatX(nu))
30493038
self.mean = mu + nu
30503039
self.variance = (sigma ** 2) + (nu ** 2)
@@ -3317,12 +3306,11 @@ def __init__(self, mu=0.0, sigma=None, tau=None, alpha=1, sd=None, *args, **kwar
33173306

33183307
if sd is not None:
33193308
sigma = sd
3320-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
33213309

33223310
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
33233311
self.mu = mu = tt.as_tensor_variable(floatX(mu))
33243312
self.tau = tt.as_tensor_variable(tau)
3325-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
3313+
self.sigma = tt.as_tensor_variable(sigma)
33263314

33273315
self.alpha = alpha = tt.as_tensor_variable(floatX(alpha))
33283316

@@ -3721,11 +3709,10 @@ def __init__(self, nu=None, sigma=None, b=None, sd=None, *args, **kwargs):
37213709
super().__init__(*args, **kwargs)
37223710
if sd is not None:
37233711
sigma = sd
3724-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
37253712

37263713
nu, b, sigma = self.get_nu_b(nu, b, sigma)
37273714
self.nu = nu = tt.as_tensor_variable(floatX(nu))
3728-
self.sigma = self.sd = sigma = tt.as_tensor_variable(floatX(sigma))
3715+
self.sigma = sigma = tt.as_tensor_variable(floatX(sigma))
37293716
self.b = b = tt.as_tensor_variable(floatX(b))
37303717

37313718
nu_sigma_ratio = -(nu ** 2) / (2 * sigma ** 2)
@@ -3994,10 +3981,9 @@ class LogitNormal(UnitContinuous):
39943981
def __init__(self, mu=0, sigma=None, tau=None, sd=None, **kwargs):
39953982
if sd is not None:
39963983
sigma = sd
3997-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
39983984
self.mu = mu = tt.as_tensor_variable(floatX(mu))
39993985
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
4000-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
3986+
self.sigma = tt.as_tensor_variable(sigma)
40013987
self.tau = tau = tt.as_tensor_variable(tau)
40023988

40033989
self.median = invlogit(mu)

‎pymc3/distributions/mixture.py

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,6 @@
1212
# See the License for the specific language governing permissions and
1313
# limitations under the License.
1414

15-
import warnings
16-
1715
from collections.abc import Iterable
1816

1917
import numpy as np
@@ -632,11 +630,10 @@ class NormalMixture(Mixture):
632630
def __init__(self, w, mu, sigma=None, tau=None, sd=None, comp_shape=(), *args, **kwargs):
633631
if sd is not None:
634632
sigma = sd
635-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
636633
_, sigma = get_tau_sigma(tau=tau, sigma=sigma)
637634

638635
self.mu = mu = tt.as_tensor_variable(mu)
639-
self.sigma = self.sd = sigma = tt.as_tensor_variable(sigma)
636+
self.sigma = sigma = tt.as_tensor_variable(sigma)
640637

641638
super().__init__(w, Normal.dist(mu, sigma=sigma, shape=comp_shape), *args, **kwargs)
642639

‎pymc3/distributions/timeseries.py

Lines changed: 2 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -12,8 +12,6 @@
1212
# See the License for the specific language governing permissions and
1313
# limitations under the License.
1414

15-
import warnings
16-
1715
import numpy as np
1816
import theano.tensor as tt
1917

@@ -116,10 +114,9 @@ def __init__(
116114
super().__init__(*args, **kwargs)
117115
if sd is not None:
118116
sigma = sd
119-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
120117

121118
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
122-
self.sigma = self.sd = tt.as_tensor_variable(sigma)
119+
self.sigma = tt.as_tensor_variable(sigma)
123120
self.tau = tt.as_tensor_variable(tau)
124121

125122
self.mean = tt.as_tensor_variable(0.0)
@@ -211,11 +208,10 @@ def __init__(self, tau=None, init=Flat.dist(), sigma=None, mu=0.0, sd=None, *arg
211208
raise TypeError("GaussianRandomWalk must be supplied a non-zero shape argument!")
212209
if sd is not None:
213210
sigma = sd
214-
warnings.warn("sd is deprecated, use sigma instead", DeprecationWarning)
215211
tau, sigma = get_tau_sigma(tau=tau, sigma=sigma)
216212
self.tau = tt.as_tensor_variable(tau)
217213
sigma = tt.as_tensor_variable(sigma)
218-
self.sigma = self.sd = sigma
214+
self.sigma = sigma
219215
self.mu = tt.as_tensor_variable(mu)
220216
self.init = init
221217
self.mean = tt.as_tensor_variable(0.0)

‎pymc3/tests/test_glm.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ def test_linear_component(self):
7373

7474
assert round(abs(np.mean(trace["Intercept"]) - self.intercept), 1) == 0
7575
assert round(abs(np.mean(trace["x"]) - self.slope), 1) == 0
76-
assert round(abs(np.mean(trace["sigma"]) - self.sd), 1) == 0
76+
assert round(abs(np.mean(trace["sigma"]) - self.sigma), 1) == 0
7777

7878
def test_glm(self):
7979
with Model() as model:
@@ -83,7 +83,7 @@ def test_glm(self):
8383

8484
assert round(abs(np.mean(trace["Intercept"]) - self.intercept), 1) == 0
8585
assert round(abs(np.mean(trace["x"]) - self.slope), 1) == 0
86-
assert round(abs(np.mean(trace["sd"]) - self.sd), 1) == 0
86+
assert round(abs(np.mean(trace["sd"]) - self.sigma), 1) == 0
8787

8888
def test_glm_offset(self):
8989
offset = 1.0

‎pymc3/tests/test_models_linear.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -59,7 +59,7 @@ def test_linear_component(self):
5959

6060
assert round(abs(np.mean(trace["lm_Intercept"]) - self.intercept), 1) == 0
6161
assert round(abs(np.mean(trace["lm_x0"]) - self.slope), 1) == 0
62-
assert round(abs(np.mean(trace["sigma"]) - self.sd), 1) == 0
62+
assert round(abs(np.mean(trace["sigma"]) - self.sigma), 1) == 0
6363
assert vars_to_create == set(model.named_vars.keys())
6464

6565
def test_linear_component_from_formula(self):
@@ -75,7 +75,7 @@ def test_linear_component_from_formula(self):
7575

7676
assert round(abs(np.mean(trace["Intercept"]) - self.intercept), 1) == 0
7777
assert round(abs(np.mean(trace["x"]) - self.slope), 1) == 0
78-
assert round(abs(np.mean(trace["sigma"]) - self.sd), 1) == 0
78+
assert round(abs(np.mean(trace["sigma"]) - self.sigma), 1) == 0
7979

8080
def test_glm(self):
8181
with Model() as model:
@@ -88,7 +88,7 @@ def test_glm(self):
8888
)
8989
assert round(abs(np.mean(trace["glm_Intercept"]) - self.intercept), 1) == 0
9090
assert round(abs(np.mean(trace["glm_x0"]) - self.slope), 1) == 0
91-
assert round(abs(np.mean(trace["glm_sd"]) - self.sd), 1) == 0
91+
assert round(abs(np.mean(trace["glm_sd"]) - self.sigma), 1) == 0
9292
assert vars_to_create == set(model.named_vars.keys())
9393

9494
def test_glm_from_formula(self):
@@ -103,7 +103,7 @@ def test_glm_from_formula(self):
103103

104104
assert round(abs(np.mean(trace["%s_Intercept" % NAME]) - self.intercept), 1) == 0
105105
assert round(abs(np.mean(trace["%s_x" % NAME]) - self.slope), 1) == 0
106-
assert round(abs(np.mean(trace["%s_sd" % NAME]) - self.sd), 1) == 0
106+
assert round(abs(np.mean(trace["%s_sd" % NAME]) - self.sigma), 1) == 0
107107

108108
def test_strange_types(self):
109109
with Model():

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