Clean up more warnings from the test suite

Author: Armavica

pymc/tests/test_distributions.py

@@ -2077,12 +2077,13 @@ def test_mvt(self, n):
 
     @pytest.mark.parametrize("n", [2, 3])
     def test_wishart(self, n):
-        check_logp(
-            Wishart,
-            PdMatrix(n),
-            {"nu": Domain([0, 3, 4, np.inf], "int64"), "V": PdMatrix(n)},
-            lambda value, nu, V: scipy.stats.wishart.logpdf(value, int(nu), V),
-        )
+        with pytest.warns(UserWarning, match="Wishart distribution can currently not be used"):
+            check_logp(
+                Wishart,
+                PdMatrix(n),
+                {"nu": Domain([0, 3, 4, np.inf], "int64"), "V": PdMatrix(n)},
+                lambda value, nu, V: scipy.stats.wishart.logpdf(value, int(nu), V),
+            )
 
     @pytest.mark.parametrize("x,eta,n,lp", LKJ_CASES)
     def test_lkjcorr(self, x, eta, n, lp):

pymc/tests/test_distributions_random.py

@@ -230,7 +230,11 @@ class BaseTestDistributionRandom(SeededTest):
 
     def test_distribution(self):
         self.validate_tests_list()
-        self._instantiate_pymc_rv()
+        if self.pymc_dist == pm.Wishart:
+            with pytest.warns(UserWarning, match="can currently not be used for MCMC sampling"):
+                self._instantiate_pymc_rv()
+        else:
+            self._instantiate_pymc_rv()
         if self.reference_dist is not None:
             self.reference_dist_draws = self.reference_dist()(
                 size=self.size, **self.reference_dist_params
@@ -240,7 +244,11 @@ def test_distribution(self):
                 raise ValueError(
                     "Custom check cannot start with `test_` or else it will be executed twice."
                 )
-            getattr(self, check_name)()
+            if self.pymc_dist == pm.Wishart and check_name.startswith("check_rv_size"):
+                with pytest.warns(UserWarning, match="can currently not be used for MCMC sampling"):
+                    getattr(self, check_name)()
+            else:
+                getattr(self, check_name)()
 
     def _instantiate_pymc_rv(self, dist_params=None):
         params = dist_params if dist_params else self.pymc_dist_params

pymc/tests/test_distributions_timeseries.py

@@ -11,6 +11,8 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
+import warnings
+
 import aesara
 import numpy as np
 import pytest
@@ -125,7 +127,7 @@ def check_rv_inferred_size(self):
 
         def test_steps_scalar_check(self):
             with pytest.raises(ValueError, match="steps must be an integer scalar"):
-                self.pymc_dist.dist(steps=[1])
+                self.pymc_dist.dist(steps=[1], init_dist=pm.DiracDelta.dist(0))
 
     def test_gaussianrandomwalk_inference(self):
         mu, sigma, steps = 2, 1, 1000
@@ -136,7 +138,9 @@ def test_gaussianrandomwalk_inference(self):
             _sigma = pm.Uniform("sigma", 0, 10)
 
             obs_data = pm.MutableData("obs_data", obs)
-            grw = GaussianRandomWalk("grw", _mu, _sigma, steps=steps, observed=obs_data)
+            grw = GaussianRandomWalk(
+                "grw", _mu, _sigma, steps=steps, observed=obs_data, init_dist=Normal.dist(0, 100)
+            )
 
             trace = pm.sample(chains=1)
 
@@ -147,26 +151,30 @@ def test_gaussianrandomwalk_inference(self):
     @pytest.mark.parametrize("init", [None, pm.Normal.dist()])
     def test_gaussian_random_walk_init_dist_shape(self, init):
         """Test that init_dist is properly resized"""
-        grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init)
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == ()
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore", "Initial distribution not specified.*", UserWarning)
+            grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init)
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == ()
 
-        grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, size=(5,))
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == (5,)
+            grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, size=(5,))
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == (5,)
 
-        grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, shape=2)
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == ()
+            grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, shape=2)
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == ()
 
-        grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, shape=(5, 2))
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == (5,)
+            grw = pm.GaussianRandomWalk.dist(mu=0, sigma=1, steps=1, init_dist=init, shape=(5, 2))
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == (5,)
 
-        grw = pm.GaussianRandomWalk.dist(mu=[0, 0], sigma=1, steps=1, init_dist=init)
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == (2,)
+            grw = pm.GaussianRandomWalk.dist(mu=[0, 0], sigma=1, steps=1, init_dist=init)
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == (2,)
 
-        grw = pm.GaussianRandomWalk.dist(mu=0, sigma=[1, 1], steps=1, init_dist=init)
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == (2,)
+            grw = pm.GaussianRandomWalk.dist(mu=0, sigma=[1, 1], steps=1, init_dist=init)
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == (2,)
 
-        grw = pm.GaussianRandomWalk.dist(mu=np.zeros((3, 1)), sigma=[1, 1], steps=1, init_dist=init)
-        assert tuple(grw.owner.inputs[-2].shape.eval()) == (3, 2)
+            grw = pm.GaussianRandomWalk.dist(
+                mu=np.zeros((3, 1)), sigma=[1, 1], steps=1, init_dist=init
+            )
+            assert tuple(grw.owner.inputs[-2].shape.eval()) == (3, 2)
 
     def test_shape_ellipsis(self):
         grw = pm.GaussianRandomWalk.dist(
@@ -184,28 +192,28 @@ def test_gaussianrandomwalk_broadcasted_by_init_dist(self):
 
     @pytest.mark.parametrize("shape", ((6,), (3, 6)))
     def test_inferred_steps_from_shape(self, shape):
-        x = GaussianRandomWalk.dist(shape=shape)
+        x = GaussianRandomWalk.dist(shape=shape, init_dist=Normal.dist(0, 100))
         steps = x.owner.inputs[-1]
         assert steps.eval() == 5
 
     @pytest.mark.parametrize("shape", (None, (5, ...)))
     def test_missing_steps(self, shape):
         with pytest.raises(ValueError, match="Must specify steps or shape parameter"):
-            GaussianRandomWalk.dist(shape=shape)
+            GaussianRandomWalk.dist(shape=shape, init_dist=Normal.dist(0, 100))
 
     def test_inconsistent_steps_and_shape(self):
         with pytest.raises(AssertionError, match="Steps do not match last shape dimension"):
-            x = GaussianRandomWalk.dist(steps=12, shape=45)
+            x = GaussianRandomWalk.dist(steps=12, shape=45, init_dist=Normal.dist(0, 100))
 
     def test_inferred_steps_from_dims(self):
         with pm.Model(coords={"batch": range(5), "steps": range(20)}):
-            x = GaussianRandomWalk("x", dims=("batch", "steps"))
+            x = GaussianRandomWalk("x", dims=("batch", "steps"), init_dist=Normal.dist(0, 100))
         steps = x.owner.inputs[-1]
         assert steps.eval() == 19
 
     def test_inferred_steps_from_observed(self):
         with pm.Model():
-            x = GaussianRandomWalk("x", observed=np.zeros(10))
+            x = GaussianRandomWalk("x", observed=np.zeros(10), init_dist=Normal.dist(0, 100))
         steps = x.owner.inputs[-1]
         assert steps.eval() == 9
 

pymc/tests/test_mixture.py

@@ -337,9 +337,9 @@ def test_component_choice_random(self):
     @pytest.mark.parametrize(
         "comp_dists",
         (
-            [Normal.dist(size=(2,))],
+            Normal.dist(size=(2,)),
             [Normal.dist(), Normal.dist()],
-            [MvNormal.dist(np.ones(3), np.eye(3), size=(2,))],
+            MvNormal.dist(np.ones(3), np.eye(3), size=(2,)),
             [
                 MvNormal.dist(np.ones(3), np.eye(3)),
                 MvNormal.dist(np.ones(3), np.eye(3)),
@@ -348,7 +348,10 @@ def test_component_choice_random(self):
     )
     def test_components_expanded_by_weights(self, comp_dists):
         """Test that components are expanded when size or weights are larger than components"""
-        univariate = comp_dists[0].owner.op.ndim_supp == 0
+        if isinstance(comp_dists, list):
+            univariate = comp_dists[0].owner.op.ndim_supp == 0
+        else:
+            univariate = comp_dists.owner.op.ndim_supp == 0
 
         mix = Mixture.dist(
             w=Dirichlet.dist([1, 1], shape=(3, 2)),
@@ -371,9 +374,9 @@ def test_components_expanded_by_weights(self, comp_dists):
     @pytest.mark.parametrize(
         "comp_dists",
         (
-            [Normal.dist(size=(2,))],
+            Normal.dist(size=(2,)),
             [Normal.dist(), Normal.dist()],
-            [MvNormal.dist(np.ones(3), np.eye(3), size=(2,))],
+            MvNormal.dist(np.ones(3), np.eye(3), size=(2,)),
             [
                 MvNormal.dist(np.ones(3), np.eye(3)),
                 MvNormal.dist(np.ones(3), np.eye(3)),
@@ -382,7 +385,10 @@ def test_components_expanded_by_weights(self, comp_dists):
     )
     @pytest.mark.parametrize("expand", (False, True))
     def test_change_size(self, comp_dists, expand):
-        univariate = comp_dists[0].owner.op.ndim_supp == 0
+        if isinstance(comp_dists, list):
+            univariate = comp_dists[0].owner.op.ndim_supp == 0
+        else:
+            univariate = comp_dists.owner.op.ndim_supp == 0
 
         mix = Mixture.dist(w=Dirichlet.dist([1, 1]), comp_dists=comp_dists)
         mix = Mixture.change_size(mix, new_size=(4,), expand=expand)
@@ -444,6 +450,7 @@ def test_single_poisson_sampling(self):
             step = Metropolis()
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", "More chains .* than draws.*", UserWarning)
+                warnings.filterwarnings("ignore", "overflow encountered in exp", RuntimeWarning)
                 trace = sample(
                     5000,
                     step,
@@ -467,6 +474,7 @@ def test_list_poissons_sampling(self):
             Mixture("x_obs", w, [Poisson.dist(mu[0]), Poisson.dist(mu[1])], observed=pois_x)
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", "More chains .* than draws.*", UserWarning)
+                warnings.filterwarnings("ignore", "overflow encountered in exp", RuntimeWarning)
                 trace = sample(
                     5000,
                     chains=1,
@@ -497,6 +505,7 @@ def test_list_normals_sampling(self):
             )
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", "More chains .* than draws.*", UserWarning)
+                warnings.filterwarnings("ignore", "overflow encountered in exp", RuntimeWarning)
                 trace = sample(
                     5000,
                     chains=1,
@@ -755,6 +764,7 @@ def test_normal_mixture_sampling(self):
             step = Metropolis()
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", "More chains .* than draws.*", UserWarning)
+                warnings.filterwarnings("ignore", "overflow encountered in exp", RuntimeWarning)
                 trace = sample(
                     5000,
                     step,
@@ -989,7 +999,8 @@ def test_with_multinomial(self, batch_shape):
         w = np.ones(self.mixture_comps) / self.mixture_comps
         mixture_axis = len(batch_shape)
         with Model() as model:
-            comp_dists = Multinomial.dist(p=p, n=n, shape=(*batch_shape, self.mixture_comps, 3))
+            with pytest.warns(UserWarning, match="parameters sum up to"):
+                comp_dists = Multinomial.dist(p=p, n=n, shape=(*batch_shape, self.mixture_comps, 3))
             mixture = Mixture(
                 "mixture",
                 w=w,

pymc/tests/test_model.py

@@ -14,8 +14,6 @@
 import unittest
 import warnings
 
-from functools import reduce
-
 import aesara
 import aesara.sparse as sparse
 import aesara.tensor as at
@@ -354,7 +352,8 @@ def test_missing_data(self):
 
         res = [gf(DictToArrayBijection.map(Point(pnt, model=m))) for i in range(5)]
 
-        assert reduce(lambda x, y: np.array_equal(x, y) and y, res) is not False
+        # Assert that all the elements of res are equal
+        assert res[1:] == res[:-1]
 
     def test_aesara_switch_broadcast_edge_cases_1(self):
         # Tests against two subtle issues related to a previous bug in Theano

pymc/tests/test_ode.py

@@ -366,6 +366,9 @@ def system(y, t, p):
             with aesara.config.change_flags(mode=fast_unstable_sampling_mode):
                 with warnings.catch_warnings():
                     warnings.filterwarnings("ignore", ".*number of samples.*", UserWarning)
+                    warnings.filterwarnings(
+                        "ignore", "invalid value encountered in log", RuntimeWarning
+                    )
                     idata = pm.sample(50, tune=0, chains=1)
 
         assert idata.posterior["alpha"].shape == (1, 50)
@@ -399,6 +402,9 @@ def system(y, t, p):
             with aesara.config.change_flags(mode=fast_unstable_sampling_mode):
                 with warnings.catch_warnings():
                     warnings.filterwarnings("ignore", ".*number of samples.*", UserWarning)
+                    warnings.filterwarnings(
+                        "ignore", "invalid value encountered in log", RuntimeWarning
+                    )
                     idata = pm.sample(50, tune=0, chains=1)
 
         assert idata.posterior["alpha"].shape == (1, 50)
@@ -443,6 +449,9 @@ def system(y, t, p):
             with aesara.config.change_flags(mode=fast_unstable_sampling_mode):
                 with warnings.catch_warnings():
                     warnings.filterwarnings("ignore", ".*number of samples.*", UserWarning)
+                    warnings.filterwarnings(
+                        "ignore", "invalid value encountered in log", RuntimeWarning
+                    )
                     idata = pm.sample(50, tune=0, chains=1)
 
         assert idata.posterior["R"].shape == (1, 50)
@@ -486,6 +495,9 @@ def system(y, t, p):
             with aesara.config.change_flags(mode=fast_unstable_sampling_mode):
                 with warnings.catch_warnings():
                     warnings.filterwarnings("ignore", ".*number of samples.*", UserWarning)
+                    warnings.filterwarnings(
+                        "ignore", "invalid value encountered in log", RuntimeWarning
+                    )
                     idata = pm.sample(50, tune=0, chains=1)
 
         assert idata.posterior["beta"].shape == (1, 50)

pymc/tests/test_shape_handling.py

@@ -110,10 +110,14 @@ class TestShapesBroadcasting:
         ids=str,
     )
     def test_type_check_raises(self, bad_input):
-        with pytest.raises(TypeError):
-            shapes_broadcasting(bad_input, tuple(), raise_exception=True)
-        with pytest.raises(TypeError):
-            shapes_broadcasting(bad_input, tuple(), raise_exception=False)
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore", ".*ragged nested sequences.*", np.VisibleDeprecationWarning
+            )
+            with pytest.raises(TypeError):
+                shapes_broadcasting(bad_input, tuple(), raise_exception=True)
+            with pytest.raises(TypeError):
+                shapes_broadcasting(bad_input, tuple(), raise_exception=False)
 
     def test_type_check_success(self):
         inputs = [3, 3.0, tuple(), [3], (3,), np.array(3), np.array([3])]