Reintroduced and refactored some unit tests

MDANSE/Core/Preferences.py

@@ -305,12 +305,18 @@ class Preferences(object):
         except KeyError:
             raise PreferencesError("Unknown preferences item")
         
-    def load(self):
+    def load(self, path=None):
         '''
-        Load the preferences.
+        Load the preferences from an existing Preferences file.
+
+        The default value is the default location for loading Preferences file.
+        
+        :param path: the path for the preferences file
+        :type path: str   
         '''
                     
-        path = PLATFORM.preferences_file()
+        if path is None:
+            path = PLATFORM.preferences_file()
 
         if not isinstance(path,basestring):
             raise PreferencesError("Invalid type for preferences filename: %s" % path)
@@ -328,12 +334,18 @@ class Preferences(object):
             for k, v in self._parser.items(s):
                 self.set_preferences_item(k,v) 
                          
-    def save(self):
+    def save(self,path=None):
         '''
-        Save the preferences.        
+        Save the preferences to a file.
+        
+        The default value is the default location for loading Preferences file.
+        
+        :param path: the path for the preferences file
+        :type path: str   
         '''
         
-        path = PLATFORM.preferences_file()
+        if path is None:
+            path = PLATFORM.preferences_file()
             
         try:
             f = open(path, "w")

Tests/UnitTests/AllTests.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import unittest
+import os
+import glob
+
+def suite():
+    files = glob.glob('Test*.py')
+    modules = [__import__(os.path.splitext(f)[0],globals(),locals(),[],-1) for f in files]
+    test_suite = unittest.TestSuite()
+    for m in modules:
+        test_suite.addTests(m.suite())
+
+    return test_suite
+
+def run_test():
+    unittest.TextTestRunner(verbosity=2).run(suite())
+
+if __name__ == '__main__':
+    run_test()

Tests/UnitTests/TestElementsDatabase.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import unittest
+
+from UnitTest import UnitTest
+
+from MDANSE import ELEMENTS
+from MDANSE.Data.ElementsDatabase import ElementsDatabaseError
+
+class TestElementsDatabase(UnitTest):
+    '''
+    Unittest for the configurators used to setup an analysis in nMolDyn
+    '''
+    
+    def setUp(self):
+        
+        self._types = {float:1.0,int:1,str:"toto"}
+    
+
+    def test___contains__(self):
+        
+        self.assertFalse("fhsdjfsd" in ELEMENTS)
+        self.assertFalse("h" in ELEMENTS)
+        self.assertTrue("H" in ELEMENTS)
+
+    def test___getitem__(self):
+                
+        for e in ELEMENTS.elements:
+            for p in ELEMENTS.properties:
+                self.assertNotRaises(ELEMENTS.__getitem__,(e,p))
+
+    def test_getelement(self):
+        
+        for e in ELEMENTS.elements:
+            self.assertNotRaises(ELEMENTS.get_element,e)
+
+    def test_get_property(self):
+                
+        for p in ELEMENTS.properties:
+            self.assertNotRaises(ELEMENTS.get_property,p)
+
+    def test___setitem__(self):
+        
+        self.assertNotRaises(ELEMENTS.__setitem__,('C','atomic_weight'),20.0)
+                                
+    def test_add_element(self):
+        
+        # Adding an already existing element does not trigger an error anymore
+        self.assertNotRaises(ELEMENTS.add_element, "H")
+
+        # Otherwise, everything should be OK
+        self.assertNotRaises(ELEMENTS.add_element, "element1")
+        
+    def test_add_property(self):
+        
+        # Adding an already existing property must trigger an error
+        self.assertRaises(ElementsDatabaseError, ELEMENTS.add_property, "atomic_weight",0.0)
+                
+        # Otherwise, everything should be OK
+        self.assertNotRaises(ELEMENTS.add_property, "prop1",'float')
+        self.assertNotRaises(ELEMENTS.add_property, "prop2",'int')
+        self.assertNotRaises(ELEMENTS.add_property, "prop3",'str')
+        
+    def test_has_property(self):
+        
+        for p in ELEMENTS.properties:
+            self.assertTrue(ELEMENTS.has_property(p))
+            
+        self.assertFalse(ELEMENTS.has_property("gfkljfklsj"))
+            
+    def test_has_element(self):
+        
+        for e in ELEMENTS.elements:
+            self.assertTrue(ELEMENTS.has_element(e))
+            
+        self.assertFalse(ELEMENTS.has_element("gfkljfklsj"))
+            
+def suite():
+    loader = unittest.TestLoader()
+    s = unittest.TestSuite()
+    s.addTest(loader.loadTestsFromTestCase(TestElementsDatabase))
+    return s
+
+if __name__ == '__main__':
+    unittest.main(verbosity=2)
+            
+        
\ No newline at end of file

Tests/UnitTests/TestGeometry.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import unittest
+
+import numpy
+
+from UnitTest import UnitTest
+
+from MDANSE.Mathematics.Geometry import center_of_mass
+
+class TestGeometry(UnitTest):
+    '''
+    Unittest for the geometry-related functions
+    '''
+        
+    def test_center_of_mass(self):
+        
+        coords = numpy.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]],dtype=numpy.float64)
+
+        self.assertTrue(numpy.array_equal(center_of_mass(coords),numpy.array([0.5,0.5,0.5],dtype=numpy.float64)))
+
+        masses = numpy.array([1.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0],dtype=numpy.float64)
+        self.assertTrue(numpy.array_equal(center_of_mass(coords,masses=masses),numpy.array([0.5,0.5,0.0],dtype=numpy.float64)))
+        
+            
+def suite():
+    loader = unittest.TestLoader()
+    s = unittest.TestSuite()
+    s.addTest(loader.loadTestsFromTestCase(TestGeometry))
+    return s
+
+if __name__ == '__main__':
+    unittest.main(verbosity=2)
+            
+        
\ No newline at end of file

Tests/UnitTests/TestMolecularDynamics.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import unittest
+
+import numpy
+
+from UnitTest import UnitTest
+
+from MDANSE.MolecularDynamics.Analysis import radius_of_gyration, mean_square_deviation, mean_square_fluctuation
+
+class TestMolecularDynamics(UnitTest):
+    '''
+    Unittest for the geometry-related functions
+    '''
+                
+    def test_radius_of_gyration(self):
+
+        coords = numpy.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]],dtype=numpy.float64)        
+        self.assertEqual(radius_of_gyration(coords,root=True),numpy.sqrt(0.75))
+
+        masses = numpy.array([1.0,1.0,1.0,1.0,0.0,0.0,0.0,0.0],dtype=numpy.float64)
+        self.assertEqual(radius_of_gyration(coords,masses=masses,root=True),numpy.sqrt(0.5))
+
+    def test_mean_square_deviation(self):
+
+        coords1 = numpy.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]],dtype=numpy.float64)        
+
+        coords2 = numpy.array([[1,1,1],[2,1,1],[2,2,1],[1,2,1],[1,1,2],[2,1,2],[2,2,2],[1,2,2]],dtype=numpy.float64)        
+            
+        self.assertEqual(mean_square_deviation(coords1,coords2,root=True),numpy.sqrt(3))
+
+        self.assertEqual(mean_square_deviation(coords1,coords2,root=False),3)
+            
+    def test_mean_square_fluctuation(self):
+
+        coords = numpy.array([[0,0,0],[1,0,0],[1,1,0],[0,1,0],[0,0,1],[1,0,1],[1,1,1],[0,1,1]],dtype=numpy.float64)        
+                        
+        self.assertEqual(mean_square_fluctuation(coords,root=False),0.75)
+            
+def suite():
+    loader = unittest.TestLoader()
+    s = unittest.TestSuite()
+    s.addTest(loader.loadTestsFromTestCase(TestMolecularDynamics))
+    return s
+
+if __name__ == '__main__':
+    unittest.main(verbosity=2)
+            
+        
\ No newline at end of file

Tests/UnitTests/TestPreferences.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import os
+import unittest
+
+# The nmoldyn imports
+from MDANSE import PREFERENCES
+from MDANSE.Core.Preferences import PreferencesError
+from UnitTest import UnitTest
+
+class UnStringable:
+    
+    def __str__(self):        
+        raise TypeError("Object not castable to a string.")
+
+class TestPreferences(UnitTest):
+    
+    def test_get_item(self):
+        
+        self.assertRaises(PreferencesError,PREFERENCES.get_preferences_item,'xxxxx')
+
+    def test_set_item(self):
+        
+        val = PREFERENCES.get_preferences_item("working_directory")
+        PREFERENCES.set_preferences_item("working_directory","test")
+        self.assertEqual(PREFERENCES.get_preferences_item("working_directory").value,os.path.join(os.getcwd(),"test"))
+        PREFERENCES.set_preferences_item("working_directory",val)
+                
+    def test_load_preferences(self):
+        '''
+        Test the method that loads the preferences
+        '''
+        
+        # Test that loading a preferences file whose type is not a basestring throw a PreferencesError
+        self.assertRaises(PreferencesError,PREFERENCES.load,10)
+
+    def test_save_preferences(self):
+        '''
+        Test the method that saves the preferences
+        '''
+        
+        # Test that saving a preferences file whose type is not a basestring throw a PreferencesError
+        self.assertRaises(PreferencesError,PREFERENCES.save,10)
+        # Test that saving a preferences whose path does not exists throw a PreferencesError
+        self.assertRaises(PreferencesError,PREFERENCES.save,os.path.join('xxxx','yyyy'))
+
+def suite():
+    loader = unittest.TestLoader()
+    s = unittest.TestSuite()
+    s.addTest(loader.loadTestsFromTestCase(TestPreferences))
+    return s
+
+if __name__ == '__main__':
+    unittest.main(verbosity=2)

Tests/UnitTests/UnitTest.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library 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
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on May 29, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import sys
+import unittest
+
+class UnitTest(unittest.TestCase):
+
+    def assertNotRaises(self, callableObj, *args, **kwargs):
+        try:
+            callableObj(*args, **kwargs)
+        except:
+            self.fail(sys.exc_info())