add solvent extractor and test.

phasecalculator/io/solventextractor.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+"""
+Script for spliting input fed into different energy XML files based on solvent ID.
+
+@author: mark
+"""
+
+import logging
+import solventmapcreator.io.solvationenergyextraction as solvextract
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+def extract_and_write_energy_values_from_files(solvent_filename, energy_xml_filename, energy_type, directory):
+    """Extracts energies and splits to different file for each solvent.
+
+    Parameters
+    ----------
+    solvent_filename : str
+        Solvent XML filename.
+    energy_xml_filename : str
+        Energy XML filename.
+    energy_type : str
+        type of energy to extract. Either "binding" or "free".
+    directory : str
+        directory name.
+
+    Returns
+    -------
+    None
+        Result in file output to disk.
+
+    """
+    solvextract.extract_and_write_energy_values_from_files(solvent_filename, energy_xml_filename, energy_type, directory)
+
+

phasecalculator/test/iotest/solventextractortest.py

+# -*- coding: utf-8 -*-
+#    phasecalculator calculates FGIPs, solvent similarity and VLE with SSIMPLE.
+#    Copyright (C) 2019  Mark D. Driver
+#
+#    phasecalculator is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU Affero General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU Affero General Public License for more details.
+#
+#    You should have received a copy of the GNU Affero General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+"""
+Test case for solvent extractor method.
+
+@author: Mark
+"""
+
+import logging
+import unittest
+import pathlib
+import os
+import phasecalculator.io.solventextractor as solvextract
+
+logging.basicConfig()
+LOGGER = logging.getLogger(__name__)
+LOGGER.setLevel(logging.WARN)
+
+class SolventExtractorTestCase(unittest.TestCase):
+    """Test case for solvent extractor methods."""
+    def setUp(self):
+        """Set up for tests.
+
+        Returns
+        -------
+        None.
+
+        """
+        self.maxDiff = None
+        parent_directory = pathlib.Path(__file__).parents[1]
+        self.binding_energy_filename = (
+            (parent_directory / "resources/expected_bindingenergy.xml").absolute().as_posix()
+        )
+        self.expected_output_filename = (
+            (parent_directory / "resources/expected_bindingparsed.xml").absolute().as_posix()
+        ) 
+        self.output_filename = "1-butanol0.165water0.835binding.xml"
+        self.solvent_filename = (
+            (parent_directory / "resources/expected_solvent.xml").absolute().as_posix()
+        )
+    def tearDown(self):
+        """Clean up after tests.
+
+        Returns
+        -------
+        None.
+
+        """
+        if os.path.isfile(self.output_filename):
+            os.remove(self.output_filename)
+        del self.output_filename
+        
+    def test_extract_and_write_energy_values_from_file(self):
+        """
+
+        Returns
+        -------
+        None.
+
+        """
+        solvextract.extract_and_write_energy_values_from_files(self.solvent_filename, self.binding_energy_filename, "binding", "")
+        with open(self.output_filename, "r") as actual_file:
+            actual_xml = actual_file.read()
+            with open(self.expected_output_filename) as expected_file:
+                expected_xml = expected_file.read()
+                self.assertMultiLineEqual(expected_xml, actual_xml)
\ No newline at end of file

phasecalculator/test/phasecalculatortests.py

@@ -15,7 +15,9 @@
 #    You should have received a copy of the GNU Affero General Public License
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 """
-Created on Tue Jan  7 16:34:17 2020
+Test runner using unittest framework.
+
+This can also be used to run tests on the installed instance of the library.
 
 @author: Mark
 """
@@ -24,14 +26,17 @@ import logging
 import unittest
 import sys
 from phasecalculator.test.iotest.phasetransferxmlcreatortest import PhasetransferXMLCreatorTestCase
+from phasecalculator.test.iotest.solventextractortest import SolventExtractorTestCase
+from phasecalculator.test.runnerstest.phasetransferrunnertest import PhasetransferRunnerTestCase
 
 logging.basicConfig()
 LOGGER = logging.getLogger(__name__)
 LOGGER.setLevel(logging.WARN)
 
-IO_TEST_CASES = [PhasetransferXMLCreatorTestCase,]
+IO_TEST_CASES = [PhasetransferXMLCreatorTestCase,
+                 SolventExtractorTestCase,]
 
-RUNNERS_TEST_CASES = []
+RUNNERS_TEST_CASES = [PhasetransferRunnerTestCase,]
 
 ANALYSIS_TEST_CASES = []