Bug fix #2279 (#2280)

* Bug fix #2279

* add_random_variable for potential and transformed
* fix typo

* fix test

* add test

test for duplicate varname

Author: Junpeng Lao

pymc3/model.py

@@ -539,6 +539,7 @@ def Var(self, name, dist, data=None, total_size=None):
                                 name=name,
                                 orig_name=get_transformed_name(name, dist.transform)))
                 self.deterministics.append(var)
+                self.add_random_variable(var)
                 return var
         elif isinstance(data, dict):
             with self:
@@ -985,7 +986,7 @@ def Deterministic(name, var, model=None):
 
     Returns
     -------
-    n : var but with name name
+    var : var, with name attribute
     """
     model = modelcontext(model)
     var.name = model.name_for(name)
@@ -1009,6 +1010,7 @@ def Potential(name, var, model=None):
     model = modelcontext(model)
     var.name = model.name_for(name)
     model.potentials.append(var)
+    model.add_random_variable(var)
     return var
 
 

pymc3/tests/test_model.py

@@ -2,7 +2,7 @@
 import scipy.stats as stats
 import numpy as np
 import pymc3 as pm
-from pymc3.distributions import HalfCauchy, Normal
+from pymc3.distributions import HalfCauchy, Normal, transforms
 from pymc3 import Potential, Deterministic
 from pymc3.theanof import generator
 from .helpers import select_by_precision
@@ -213,3 +213,28 @@ def test_nested(self):
                     assert theano.config.compute_test_value == 'warn'
                 assert theano.config.compute_test_value == 'ignore'
             assert theano.config.compute_test_value == 'off'
+
+def test_duplicate_vars():
+    with pytest.raises(ValueError) as err:
+        with pm.Model():
+            pm.Normal('a')
+            pm.Normal('a')
+    err.match('already exists')
+
+    with pytest.raises(ValueError) as err:
+        with pm.Model():
+            pm.Normal('a')
+            pm.Normal('a', transform=transforms.log)
+    err.match('already exists')
+
+    with pytest.raises(ValueError) as err:
+        with pm.Model():
+            a = pm.Normal('a')
+            pm.Potential('a', a**2)
+    err.match('already exists')
+
+    with pytest.raises(ValueError) as err:
+        with pm.Model():
+            pm.Binomial('a', 10, .5)
+            pm.Normal('a', transform=transforms.log)
+    err.match('already exists')

pymc3/tests/test_models_linear.py

@@ -30,6 +30,7 @@ def setup_class(cls):
 
     def test_linear_component(self):
         vars_to_create = {
+            'sigma',
             'sigma_interval__',
             'y_obs',
             'lm_x0',
@@ -71,6 +72,7 @@ def test_linear_component_from_formula(self):
     def test_glm(self):
         with Model() as model:
             vars_to_create = {
+                'glm_sd',
                 'glm_sd_log__',
                 'glm_y',
                 'glm_x0',