Prettify

arkane/output.py

@@ -49,16 +49,14 @@ def __init__(self, level=0, indent=4):
         self.level = level
         self.indent = indent
 
-    def visit_call(self, node):
+    def visit_Call(self, node):
         """
         Return a pretty representation of the class or function call represented by `node`.
         """
-        result = node.func.id + '(\n'
-
         keywords = []
         for keyword in node.keywords:
             keywords.append('{0}={1}'.format(keyword.arg, self.visit(keyword.value)))
-        result += '{0}({1})'.format(node.func.id, ', '.join(keywords))
+        result = '{0}({1})'.format(node.func.id, ', '.join(keywords))
 
         if len(result) > 80:
             result = node.func.id + '(\n'
@@ -75,11 +73,11 @@ def visit_call(self, node):
 
         return result
 
-    def visit_list(self, node):
+    def visit_List(self, node):
         """
         Return a pretty representation of the list represented by `node`.
         """
-        if any([not isinstance(e, (ast.Str, ast.Num)) for e in node.elts]):
+        if any([not isinstance(e, (ast.Str, ast.Num, ast.UnaryOp)) for e in node.elts]):
             # Split elements onto multiple lines
             result = '[\n'
             self.level += 1
@@ -94,14 +92,15 @@ def visit_list(self, node):
             self.string = result
             return result
 
-    def visit_tuple(self, node):
+    def visit_Tuple(self, node):
         """
         Return a pretty representation of the tuple represented by `node`.
         """
         # If the tuple represents a quantity, keep it on one line
         is_quantity = True
         if len(node.elts) == 0 or not isinstance(node.elts[0], (ast.Num, ast.List)) or (
-                isinstance(node.elts[0], ast.List) and any([not isinstance(e, ast.Num) for e in node.elts[0].elts])):
+                isinstance(node.elts[0], ast.List) and
+                any([not isinstance(e, (ast.Num, ast.UnaryOp)) for e in node.elts[0].elts])):
             is_quantity = False
         elif len(node.elts) < 2 or not isinstance(node.elts[1], ast.Str):
             is_quantity = False
@@ -121,7 +120,7 @@ def visit_tuple(self, node):
             self.string = result
             return result
 
-    def visit_dict(self, node):
+    def visit_Dict(self, node):
         """
         Return a pretty representation of the dict represented by `node`.
         """
@@ -143,15 +142,15 @@ def visit_dict(self, node):
             self.string = result
             return result
 
-    def visit_str(self, node):
+    def visit_Str(self, node):
         """
         Return a pretty representation of the string represented by `node`.
         """
         result = repr(node.s)
         self.string = result
         return result
 
-    def visit_num(self, node):
+    def visit_Num(self, node):
         """
         Return a pretty representation of the number represented by `node`.
         """
@@ -160,6 +159,18 @@ def visit_num(self, node):
         self.string = result
         return result
 
+    def visit_UnaryOp(self, node):
+        """
+        Return a pretty representation of the number represented by `node`.
+        """
+        operators = {
+            ast.UAdd: '+',
+            ast.USub: '-',
+        }
+        result = '{0}{1}'.format(operators[node.op.__class__], self.visit(node.operand))
+        self.string = result
+        return result
+
 
 def prettify(string, indent=4):
     """

arkane/outputTest.py

@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+###############################################################################
+#                                                                             #
+# RMG - Reaction Mechanism Generator                                          #
+#                                                                             #
+# Copyright (c) 2002-2019 Prof. William H. Green (whgreen@mit.edu),           #
+# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)   #
+#                                                                             #
+# 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:`arkane.gaussian` module.
+"""
+
+import os
+import shutil
+import unittest
+
+from nose.plugins.attrib import attr
+
+import rmgpy
+from arkane.main import Arkane
+from arkane.output import prettify
+
+
+@attr('functional')
+class OutputTest(unittest.TestCase):
+    """
+    Contains functional tests for Arkane's output module.
+    """
+    def test_prettify(self):
+        """Test that the prettify function works for an Arkane job"""
+        benzyl_path = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)),
+                                   'examples', 'arkane', 'species', 'Benzyl')
+
+        arkane = Arkane(input_file=os.path.join(benzyl_path, 'input.py'), output_directory=benzyl_path)
+        arkane.plot = False
+        arkane.execute()
+        with open(os.path.join(benzyl_path, 'output.py'), 'r') as f:
+            lines = f.readlines()
+        self.assertIn('conformer(\n', lines)
+        self.assertIn("    E0 = (193.749, 'kJ/mol'),\n", lines)
+        self.assertIn('thermo(\n', lines)
+        self.assertIn("        Cp0 = (33.2579, 'J/(mol*K)'),\n", lines)
+
+    @classmethod
+    def tearDownClass(cls):
+        """A function that is run ONCE after all unit tests in this class."""
+        benzyl_path = os.path.join(os.path.dirname(os.path.dirname(rmgpy.__file__)),
+                                   'examples', 'arkane', 'species', 'Benzyl')
+        extensions_to_delete = ['pdf', 'csv', 'txt', 'inp']
+        files_to_delete = ['arkane.log', 'output.py']
+        for name in os.listdir(benzyl_path):
+            item_path = os.path.join(benzyl_path, name)
+            if os.path.isfile(item_path):
+                extension = name.split('.')[-1]
+                if name in files_to_delete or extension in extensions_to_delete:
+                    os.remove(item_path)
+            else:
+                if os.path.split(item_path)[-1] in ['r0']:
+                    continue
+                # This is a sub-directory. remove.
+                shutil.rmtree(item_path)
+
+
+class OutputUnitTest(unittest.TestCase):
+    """
+    Contains unit tests for the Arkane's output module.
+    """
+    def test_prettify(self):
+        """Test that ``prettify`` returns the expected result"""
+        input_str = ("conformer(label='C7H7', E0=(193.749,'kJ/mol'), modes=[IdealGasTranslation(mass=(91.0548,'amu')), "
+                     "NonlinearRotor(inertia=([91.0567,186.675,277.733],'amu*angstrom^2'), symmetry=2), "
+                     "HarmonicOscillator(frequencies=([199.381,360.536,413.795,480.347,536.285,630.723,687.118,709.613,"
+                     "776.662,830.404,834.386,901.841,973.498,975.148,993.349,998.606,1040.14,1120.69,1179.22,1189.07,"
+                     "1292.86,1332.91,1357.18,1479.46,1495.36,1507.91,1583.14,1604.63,3156.85,3170.22,3172.78,3185.05,"
+                     "3189.8,3203.23,3253.99],'cm^-1')), HinderedRotor(inertia=(1.70013,'amu*angstrom^2'), symmetry=2, "
+                     "fourier=([[-0.315923,-27.7665,0.177678,3.2437,0.0509515],[-0.00164953,-0.0021925,-0.00386396,"
+                     "-0.000912068,0.00274206]],'kJ/mol'), quantum=True, semiclassical=False)], spin_multiplicity=2, "
+                     "optical_isomers=1)")
+        expected_output = """conformer(
+    label = 'C7H7',
+    E0 = (193.749, 'kJ/mol'),
+    modes = [
+        IdealGasTranslation(mass=(91.0548, 'amu')),
+        NonlinearRotor(
+            inertia = ([91.0567, 186.675, 277.733], 'amu*angstrom^2'),
+            symmetry = 2,
+        ),
+        HarmonicOscillator(
+            frequencies = ([199.381, 360.536, 413.795, 480.347, 536.285, 630.723, 687.118, 709.613, 776.662, 830.404, 834.386, 901.841, 973.498, 975.148, 993.349, 998.606, 1040.14, 1120.69, 1179.22, 1189.07, 1292.86, 1332.91, 1357.18, 1479.46, 1495.36, 1507.91, 1583.14, 1604.63, 3156.85, 3170.22, 3172.78, 3185.05, 3189.8, 3203.23, 3253.99], 'cm^-1'),
+        ),
+        HinderedRotor(
+            inertia = (1.70013, 'amu*angstrom^2'),
+            symmetry = 2,
+            fourier = (
+                [
+                    [-0.315923, -27.7665, 0.177678, 3.2437, 0.0509515],
+                    [-0.00164953, -0.0021925, -0.00386396, -0.000912068, 0.00274206],
+                ],
+                'kJ/mol',
+            ),
+            quantum = None,
+            semiclassical = None,
+        ),
+    ],
+    spin_multiplicity = 2,
+    optical_isomers = 1,
+)"""
+        self.assertEqual(prettify(input_str), expected_output)
+
+
+if __name__ == '__main__':
+    unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))