T3 Main Test Fix

T3 Main tests were failing due to changes in RMG-Py. This has been rectified. The first change is now we look for the numeric identifier of the species instead of the species name as the numeric identifier should never change and is unique. The second function change is that the chemical reaction string uses '<=>' instead of '='.

tests/test_main.py

@@ -8,6 +8,7 @@
 import datetime
 import os
 import shutil
+import re
 
 from rmgpy.data.thermo import ThermoLibrary
 from rmgpy.reaction import Reaction
@@ -734,7 +735,12 @@ def test_determine_species_based_on_collision_violators():
         'S(26357)',
         'S(25149)'
     ]
-    assert [t3.species[index]['Chemkin label'] for index in species_to_calc] == expected_species_to_calc
+    expected_numeric_identifiers = [int(re.findall(r'\((\d+)\)', species)[0]) for species in expected_species_to_calc]
+    numeric_identifiers = [int(re.findall(r'\((\d+)\)', t3.species[index]['Chemkin label'])[0]) for index in species_to_calc]
+
+    # Assert that the numeric identifiers are the same
+    # We do this because 'S' is a generic label for a species, and the numeric identifier is what distinguishes them
+    assert expected_numeric_identifiers == numeric_identifiers
 
 
 def test_trsh_rmg_tol():
@@ -865,7 +871,7 @@ def test_add_reaction():
 
     assert t3.get_reaction_key(reaction=rmg_reactions[342]) == 0
     assert t3.reactions[0]['RMG label'] == 's0_H + s1_CC=CCCC <=> s2_S2XC6H13'
-    assert 'H(2)+S(1229)=C6H13(794)' in t3.reactions[0]['Chemkin label']
+    assert 'H(2)+C6H12(1229)<=>S2XC6H13(794)' in t3.reactions[0]['Chemkin label']
     assert t3.reactions[0]['QM label'] == 's0_H + s1_CC=CCCC <=> s2_S2XC6H13'
     assert t3.reactions[0]['SMILES label'] == '[H] + CC=CCCC <=> CC[CH]CCC'
     assert isinstance(t3.reactions[0]['object'], Reaction)
@@ -875,7 +881,7 @@ def test_add_reaction():
 
     assert t3.get_reaction_key(reaction=rmg_reactions[100]) == 1
     assert t3.reactions[1]['RMG label'] == 's3_S2XC12H25 + s4_fuel <=> s5_S3XC12H25 + s4_fuel'
-    assert 'S(839)+fuel(1)=S(840)+fuel(1)' in t3.reactions[1]['Chemkin label']
+    assert 'S2XC12H25(839)+fuel(1)<=>S3XC12H25(840)+fuel(1)' in t3.reactions[1]['Chemkin label']
     assert t3.reactions[1]['QM label'] == 's3_S2XC12H25 + s4_fuel <=> s5_S3XC12H25 + s4_fuel'
     assert t3.reactions[1]['SMILES label'] == 'CC[CH]CCCCCCCCC + CCCCCCCCCCCC <=> CCC[CH]CCCCCCCC + CCCCCCCCCCCC'
     assert isinstance(t3.reactions[1]['object'], Reaction)
@@ -885,7 +891,7 @@ def test_add_reaction():
 
     assert t3.get_reaction_key(reaction=rmg_reactions[14]) == 2
     assert t3.reactions[2]['RMG label'] == 's6_PC4H9 <=> s7_C2H4 + s8_C2H5'
-    assert 'PC4H9(191)=C2H4(22)+C2H5(52)' in t3.reactions[2]['Chemkin label']
+    assert 'PC4H9(191)<=>C2H4(22)+C2H5(52)' in t3.reactions[2]['Chemkin label']
     assert t3.reactions[2]['QM label'] == 's6_PC4H9 <=> s7_C2H4 + s8_C2H5'
     assert t3.reactions[2]['SMILES label'] == '[CH2]CCC <=> C=C + C[CH2]'
     assert isinstance(t3.reactions[2]['object'], Reaction)