resolve some annoying warnings

Author: JacksonBurns

rmgpy/qm/gaussian.py

@@ -27,12 +27,12 @@
 #                                                                             #
 ###############################################################################
 
-import distutils.spawn
 import itertools
 import logging
 import os
 import re
 from subprocess import Popen
+import shutil
 
 import cclib
 
@@ -55,7 +55,7 @@ class Gaussian:
 
     for exe in executablesToTry:
         try:
-            executable_path = distutils.spawn.find_executable(exe)
+            executable_path = shutil.which(exe)
         except:
             executable_path = None
         if executable_path is not None:

rmgpy/qm/mopac.py

@@ -27,7 +27,6 @@
 #                                                                             #
 ###############################################################################
 
-import distutils.spawn
 import logging
 import os
 import re
@@ -52,7 +51,7 @@ class Mopac(object):
     input_file_extension = ".mop"
     output_file_extension = ".out"
 
-    executable_path = distutils.spawn.find_executable("mopac")
+    executable_path = shutil.which("mopac")
 
     use_polar = False  # use polar keyword in MOPAC
 

test/database/databaseTest.py

@@ -463,12 +463,12 @@ def kinetics_check_surface_library_reactions_have_surface_attributes(self, libra
         failed = False
         if "_Pt" in library.label:
             for entry in entries:
-                if entry.metal is not "Pt":
+                if entry.metal != "Pt":
                     logging.error(f"Expected {entry} metal attribute in {library} library to match Pt, but was {entry.metal}")
                     failed = True
         if "_Ni" in library.label:
             for entry in entries:
-                if entry.metal is not "Ni":
+                if entry.metal != "Ni":
                     logging.error(f"Expected {entry} metal attribute in {library} library to match Ni, but was {entry.metal}")
                     failed = True
         for entry in entries:
@@ -1090,7 +1090,7 @@ def kinetics_check_cd_atom_type(self, family_name):
                         continue
                     # Create list of all the atomTypes that should be present in addition or instead of Cd
                     correct_atom_list = []
-                    num_of_d_bonds = sum([1 if x.order[0] is "D" and len(x.order) == 1 else 0 for x in atom.bonds.values()])
+                    num_of_d_bonds = sum([1 if x.order[0] == "D" and len(x.order) == 1 else 0 for x in atom.bonds.values()])
                     if num_of_d_bonds == 2:
                         correct_atom_list.append("Cdd")
                     elif num_of_d_bonds == 1:
@@ -1675,11 +1675,11 @@ def check_surface_thermo_groups_have_surface_attributes(self, group_name, group)
         for entry in group.entries.values():
             if isinstance(entry.data, rmgpy.thermo.thermodata.ThermoData):
                 if "Pt" in group_name:
-                    if entry.metal is not "Pt":
+                    if entry.metal != "Pt":
                         logging.error(f"Expected {entry} metal attribute in {group_name} group to match Pt, but was {entry.metal}")
                         failed = True
                 if "111" in group_name:
-                    if entry.facet is not "111":
+                    if entry.facet != "111":
                         logging.error(f"Expected {entry} facet attribute in {group_name} group to match 111, but was {entry.facet}")
                         failed = True
                 if not entry.metal:
@@ -1701,15 +1701,15 @@ def check_surface_thermo_libraries_have_surface_attributes(self, library_name, l
         failed = False
         for entry in library.entries.values():
             if "Pt" in library_name:
-                if entry.metal is not "Pt":
+                if entry.metal != "Pt":
                     logging.error(f"Expected {entry} metal attribute in {library_name} library to match Pt, but was {entry.metal}")
                     failed = True
             if "Ni" in library_name:
-                if entry.metal is not "Ni":
+                if entry.metal != "Ni":
                     logging.error(f"Expected {entry} metal attribute in {library_name} library to match Ni, but was {entry.metal}")
                     failed = True
             if "111" in library_name:
-                if entry.facet is not "111":
+                if entry.facet != "111":
                     logging.error(f"Expected {entry} facet attribute in {library_name} library to match 111, but was {entry.facet}")
                     failed = True
             if not entry.metal:
@@ -1929,7 +1929,7 @@ def general_check_cd_atom_type(self, group_name, group):
                         continue
                     # figure out what the correct atomtype is
                     correct_atom_list = []
-                    num_of_d_bonds = sum([1 if x.order[0] is "D" and len(x.order) == 1 else 0 for x in atom.bonds.values()])
+                    num_of_d_bonds = sum([1 if x.order[0] == "D" and len(x.order) == 1 else 0 for x in atom.bonds.values()])
                     if num_of_d_bonds == 2:
                         correct_atom_list.append("Cdd")
                     elif num_of_d_bonds == 1: