Merge pull request #5 from parsing-science/Fix-some-errors-in-v2

Use bytes with joblib and remove output variable from create_model

Author: parsing-science

.gitignore

@@ -89,3 +89,5 @@ ENV/
 # Rope project settings
 .ropeproject
 
+# HLM models
+HLM_jar/

ps_toolkit/pymc3_models/HLM.py

@@ -20,7 +20,7 @@ def create_model(self):
         """
         Creates and returns the PyMC3 model.
 
-        Returns the model and the output variable. The latter is for use in ADVI minibatch.
+        Returns the model.
         """
         model_input = theano.shared(np.zeros([1, self.num_pred]))
 
@@ -54,7 +54,7 @@ def create_model(self):
 
             o = pm.Bernoulli('o', p, observed=model_output)
 
-        return model, o
+        return model
 
     def fit(self, X, y, cats, n=200000, batch_size=100):
         """
@@ -76,7 +76,7 @@ def fit(self, X, y, cats, n=200000, batch_size=100):
         num_samples, self.num_pred = X.shape
 
         if self.cached_model is None:
-            self.cached_model, o = self.create_model()
+            self.cached_model = self.create_model()
 
         with self.cached_model:
 
@@ -109,7 +109,7 @@ def predict_proba(self, X, cats, return_std=False):
         num_samples = X.shape[0]
 
         if self.cached_model is None:
-            self.cached_model, o = self.create_model()
+            self.cached_model = self.create_model()
 
         self._set_shared_vars({'model_input': X, 'model_output': np.zeros(num_samples), 'model_cats': cats})
 

ps_toolkit/pymc3_models/__init__.py

@@ -102,12 +102,12 @@ def save(self, file_prefix, custom_params=None):
 
         custom_params: Dictionary of custom parameters to save. Defaults to None
         """
-        fileObject = open(file_prefix + 'advi_trace.pickle', 'w')
+        fileObject = open(file_prefix + 'advi_trace.pickle', 'wb')
         joblib.dump(self.advi_trace, fileObject)
         fileObject.close()
 
         if custom_params:
-            fileObject = open(file_prefix + 'params.pickle', 'w')
+            fileObject = open(file_prefix + 'params.pickle', 'wb')
             joblib.dump(custom_params, fileObject)
             fileObject.close()
 

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name='PS_Toolkit',
-    version='2.0.0',
+    version='2.0.1',
     packages=find_packages(),
     include_package_data=False,
     zip_safe=False,