Addressed some of Codacy/PR Quality Review issues.

rmgpy/rmg/main.py

@@ -58,7 +58,6 @@
 from rmgpy.data.kinetics.family import KineticsFamily, TemplateReaction
 from rmgpy.rmg.pdep import PDepReaction
 
-from rmgpy.data.thermo import ThermoLibrary
 from rmgpy.data.base import Entry
 from rmgpy import settings
 
@@ -518,7 +517,6 @@ def initialize(self, **kwargs):
                 if failsSpeciesConstraints(spec):
                     if 'allowed' in self.speciesConstraints and 'input species' in self.speciesConstraints['allowed']:
                         self.speciesConstraints['explicitlyAllowedMolecules'].append(spec.molecule[0])
-                        pass
                     else:
                         raise ForbiddenStructureException("Species constraints forbids input species {0}. Please reformulate constraints, remove the species, or explicitly allow it.".format(spec.label))
 
@@ -1655,7 +1653,9 @@ def loadRMGJavaInput(self, path):
         assert len(Tlist) > 0
         assert len(Plist) > 0
         concentrationList = np.array(concentrationList)
-        assert concentrationList.shape[1] > 0  # An arbitrary number of concentrations is acceptable, and should be run for each reactor system
+        # An arbitrary number of concentrations is acceptable, and should be run for each reactor system
+        if not concentrationList.shape[1] > 0:
+            raise AssertionError()
 
         # Make a reaction system for each (T,P) combination
         for T in Tlist:

rmgpy/rmg/model.py

@@ -33,15 +33,13 @@
 """
 
 import logging
-import math
 import numpy
 import itertools
 import gc
 import os
 
 from rmgpy.display import display
 from rmgpy import settings
-import rmgpy.constants as constants
 from rmgpy.constraints import failsSpeciesConstraints
 from rmgpy.quantity import Quantity
 from rmgpy.species import Species

rmgpy/rmg/reactTest.py

@@ -35,8 +35,6 @@
 from rmgpy import settings
 from rmgpy.data.kinetics import TemplateReaction
 from rmgpy.data.rmg import RMGDatabase
-from rmgpy.molecule import Molecule
-from rmgpy.reaction import Reaction
 from rmgpy.species import Species
 
 from rmgpy.rmg.main import RMG

rmgpy/scoop_framework/util.py

@@ -40,7 +40,6 @@
 logger = None
 
 try:
-    from scoop import futures
     from scoop.futures import map, submit
     from scoop import shared
     from scoop import logger as scooplogger

rmgpy/thermo/thermoengine.py

@@ -34,7 +34,6 @@
 import logging as logging
 from rmgpy.data.rmg import getDB
 import rmgpy.constants as constants
-from rmgpy.molecule import Molecule
 from rmgpy.statmech import Conformer
 from rmgpy.thermo import Wilhoit, NASA, ThermoData
 import rmgpy.data.rmg

rmgpy/thermo/thermoengineTest.py

@@ -33,10 +33,8 @@
 """
 
 import os
-import sys
 import unittest
 import random
-from external.wip import work_in_progress
 
 from rmgpy import settings
 from rmgpy.data.rmg import RMGDatabase