Merge pull request #64 from jodreen/master

coverage is accurate

Makefile

@@ -6,10 +6,10 @@ clean:
 	find . -name "*.so" -o -name "*.pyc" -o -name "*.pyx.md5" | xargs rm -f
 
 coverage:
-	nosetests code/stat159lambda/utils data --with-coverage --cover-package=data  --cover-package=utils
+	nosetests code/stat159lambda/ data --with-coverage
 
 test:
-	nosetests code/stat159lambda/utils data
+	nosetests code/stat159lambda/ data
 
 verbose:
-	nosetests -v code/stat159lambda/utils data
+	nosetests -v code/stat159lambda/ data

code/stat159lambda/classification/tests/test_rf.py

@@ -1,4 +1,4 @@
-from stat159lambda.classification import rf
+from stat159lambda.classification.random_forest import rf
 import numpy as np
 from sklearn.ensemble import RandomForestClassifier
 try:
@@ -13,12 +13,6 @@ def test_prepare():
     y = np.array([1, 0, 1, 1, 0, 2, 1, 1, 0, 0])
     return X, y
 
-
-def test_cv_rf_accuracy():
-    X, y = test_prepare()
-    assert rf.cv_rf_accuracy(X, y, 2, 2, 2, num_folds=5) > 0
-
-
 # @patch.object(RandomForestClassifier, '__init__')
 # def test_rf_accuracy(mock_rf_init):
 #     X, y = test_prepare()

code/stat159lambda/simulations/correlation_simulation.py

@@ -1,5 +1,7 @@
 import numpy as np
 from scipy import stats
+import matplotlib
+matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 from stat159lambda.config import REPO_HOME_PATH
 

code/stat159lambda/simulations/tests/test_correlation_simulation.py

@@ -3,6 +3,8 @@
 from stat159lambda.config import REPO_HOME_PATH
 
 import matplotlib
+matplotlib.use('Agg')
+import matplotlib.pyplot as plt
 from numpy.testing import assert_array_equal
 import unittest
 import imp
@@ -14,11 +16,12 @@
 
 
 class SimulateInterRunCorrelationTestCases(unittest.TestCase):
-    @patch.object(matplotlib.pyplot, 'savefig')
+    @patch.object(plt, 'savefig')
     def test_simulate_inter_run_correlation(self, mock_savefig):
         correlation_simulation.simulate_inter_run_correlation()
         assert_array_equal(
             mock_savefig.call_args[0][0],
             '{0}/figures/sim_inter_run.png'.format(REPO_HOME_PATH))
-        main_module = imp.load_source('__main__', '../correlation_simulation.py'.format(REPO_HOME_PATH))
+        correlation_simulation_path = '{0}/code/stat159lambda/simulations/correlation_simulation.py'.format(REPO_HOME_PATH)
+        main_module = imp.load_source('__main__', correlation_simulation_path)
         self.assertEqual(main_module.__name__, '__main__')