Fix deprecation warnings.

Author: twiecki

pymc3/sampling.py

@@ -489,7 +489,7 @@ def _check_start_shape(model, start):
             # if start var has no shape
             else:
                 # if model var has a specified shape
-                if var_shape:
+                if var_shape.size > 0:
                     e += "\nExpected shape {} for var " \
                          "'{}', got scalar {}".format(
                              tuple(var_shape), var.name, start[var.name]
@@ -1523,4 +1523,4 @@ def init_nuts(init='auto', chains=1, n_init=500000, model=None,
 
     step = pm.NUTS(potential=potential, model=model, **kwargs)
 
-    return start, step
+    return start, step

pymc3/tests/test_models_utils.py

@@ -13,15 +13,15 @@ def assertMatrixLabels(self, m, l, mt=None, lt=None):
         assert np.all(
                 np.equal(
                     m.eval(),
-                    mt if mt is not None else self.data.as_matrix()
+                    mt if mt is not None else self.data.values
                 )
             )
         assert l == list(lt or self.data.columns)
 
     def test_numpy_init(self):
-        m, l = utils.any_to_tensor_and_labels(self.data.as_matrix())
+        m, l = utils.any_to_tensor_and_labels(self.data.values
         self.assertMatrixLabels(m, l, lt=['x0', 'x1'])
-        m, l = utils.any_to_tensor_and_labels(self.data.as_matrix(), labels=['x2', 'x3'])
+        m, l = utils.any_to_tensor_and_labels(self.data.values, labels=['x2', 'x3'])
         self.assertMatrixLabels(m, l, lt=['x2', 'x3'])
 
     def test_pandas_init(self):
@@ -32,42 +32,42 @@ def test_pandas_init(self):
 
     def test_dict_input(self):
         m, l = utils.any_to_tensor_and_labels(self.data.to_dict('dict'))
-        self.assertMatrixLabels(m, l, mt=self.data.as_matrix(l), lt=l)
+        self.assertMatrixLabels(m, l, mt=self.data[l].values, lt=l)
 
         m, l = utils.any_to_tensor_and_labels(self.data.to_dict('series'))
-        self.assertMatrixLabels(m, l, mt=self.data.as_matrix(l), lt=l)
+        self.assertMatrixLabels(m, l, mt=self.data[l].values, lt=l)
 
         m, l = utils.any_to_tensor_and_labels(self.data.to_dict('list'))
-        self.assertMatrixLabels(m, l, mt=self.data.as_matrix(l), lt=l)
+        self.assertMatrixLabels(m, l, mt=self.data[l].values, lt=l)
 
         inp = {k: tt.as_tensor_variable(v) for k, v in self.data.to_dict('series').items()}
         m, l = utils.any_to_tensor_and_labels(inp)
-        self.assertMatrixLabels(m, l, mt=self.data.as_matrix(l), lt=l)
+        self.assertMatrixLabels(m, l, mt=self.data[l].values, lt=l)
 
     def test_list_input(self):
-        m, l = utils.any_to_tensor_and_labels(self.data.as_matrix().tolist())
+        m, l = utils.any_to_tensor_and_labels(self.data.values.tolist())
         self.assertMatrixLabels(m, l, lt=['x0', 'x1'])
-        m, l = utils.any_to_tensor_and_labels(self.data.as_matrix().tolist(), labels=['x2', 'x3'])
+        m, l = utils.any_to_tensor_and_labels(self.data.values.tolist(), labels=['x2', 'x3'])
         self.assertMatrixLabels(m, l, lt=['x2', 'x3'])
 
     def test_tensor_input(self):
         m, l = utils.any_to_tensor_and_labels(
-            tt.as_tensor_variable(self.data.as_matrix().tolist()),
+            tt.as_tensor_variable(self.data.values.tolist()),
             labels=['x0', 'x1']
         )
         self.assertMatrixLabels(m, l, lt=['x0', 'x1'])
         m, l = utils.any_to_tensor_and_labels(
-            tt.as_tensor_variable(self.data.as_matrix().tolist()),
+            tt.as_tensor_variable(self.data.values.tolist()),
             labels=['x2', 'x3'])
         self.assertMatrixLabels(m, l, lt=['x2', 'x3'])
 
     def test_user_mistakes(self):
         # no labels for tensor variable
         with pytest.raises(
             ValueError):
-            utils.any_to_tensor_and_labels(tt.as_tensor_variable(self.data.as_matrix().tolist()))
+            utils.any_to_tensor_and_labels(tt.as_tensor_variable(self.data.values.tolist()))
         # len of labels is bad
         with pytest.raises(
             ValueError):
-            utils.any_to_tensor_and_labels(self.data.as_matrix().tolist(),
+            utils.any_to_tensor_and_labels(self.data.values.tolist(),
             labels=['x'])