Add unittest for the RMG SA Adapter

tests/rmg_saTest.py

@@ -0,0 +1,93 @@
+#!/usr/bin/env python3
+# encoding: utf-8
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2019 Prof. William H. Green ([email protected]),           #
+# Prof. Richard H. West ([email protected]) and the RMG Team ([email protected])   #
+#                                                                             #
+# Permission is hereby granted, free of charge, to any person obtaining a     #
+# copy of this software and associated documentation files (the 'Software'),  #
+# to deal in the Software without restriction, including without limitation   #
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,    #
+# and/or sell copies of the Software, and to permit persons to whom the       #
+# Software is furnished to do so, subject to the following conditions:        #
+#                                                                             #
+# The above copyright notice and this permission notice shall be included in  #
+# all copies or substantial portions of the Software.                         #
+#                                                                             #
+# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR  #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,    #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER      #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING     #
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER         #
+# DEALINGS IN THE SOFTWARE.                                                   #
+#                                                                             #
+###############################################################################
+
+"""
+This module contains unit tests of the :mod:`tandem.sa.rmg_sa` module.
+"""
+
+import os
+import shutil
+import unittest
+
+from tandem.logger import initialize_tandem_log
+from tandem.sa.rmg_sa import RMGSA
+
+################################################################################
+
+class RMGSATest(unittest.TestCase):
+    """
+    Contains unit tests for the RMGSA module, used for performing sensitivity analysis using RMG.
+    """
+    @classmethod
+    def setUpClass(cls):
+        """
+        A method that is run before all unit tests in this class.
+        """
+        # use data from the superminimal example
+        cls.observable_list = [{'label': 'H2O2', 'smiles': 'OO'}, {'label': 'H', 'smiles': '[H]'}]
+        cls.run_directory = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'data', 'rmg_sa_test', 'iteration_0')
+        cls.input_file = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'data', 'rmg_sa_test', 'input.py')
+        cls.threshold = 0.001
+        cls.verbose = False
+        cls.output_directory = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'data', 'rmg_sa_test')
+
+        initialize_tandem_log(output_directory=cls.output_directory, verbose=cls.verbose)
+
+    def test_run_sa(self):
+        RMGSA_adapter = RMGSA(observable_list=self.observable_list,
+                              run_directory=self.run_directory,
+                              input_file=self.input_file,
+                              threshold=self.threshold,
+                              verbose=self.verbose,
+                              )
+
+        sa_success = RMGSA_adapter.run_sa()
+        self.assertTrue(sa_success)
+
+    @classmethod
+    def tearDownClass(cls):
+        """
+        A method that is run after all unit tests in this class.
+        """
+        log_file = os.path.join(cls.output_directory, 't3.log')
+        if os.path.isfile(log_file):
+            os.remove(log_file)
+
+        sa_dir = os.path.join(cls.run_directory, 'sa')
+        if os.path.isdir(sa_dir):
+            shutil.rmtree(sa_dir)
+
+
+
+################################################################################
+
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))