Merge branch 'main' into slight_name_change

ReactionMechanismGenerator · Oct 27, 2023 · 1698392 · 1698392
2 parents 52674af + e099afe
commit 1698392
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diff --git a/.github/workflows/cont_int.yml b/.github/workflows/cont_int.yml
@@ -17,6 +17,17 @@ jobs:
         - name: Checkout T3
           uses: actions/checkout@v3
 
+        - name: Clean Ubuntu Image
+          uses: kfir4444/free-disk-space@main
+          with:
+            # This may remove tools actually needed - currently does not
+            tool-cache: true
+            android: true
+            dotnet: true
+            haskell: true
+            large-packages: true
+            swap-storage: true
+
         - name: Cache RMG
           id: cache-rmg
           uses: actions/cache@v2
@@ -97,7 +108,7 @@ jobs:
               conda-${{ runner.os }}--${{ runner.arch }}-rmgpyenv-${{ env.CACHE_NUMBER}}
           env:
             # Increase this value to reset cache if etc/example-environment.yml has not changed
-            CACHE_NUMBER: 0
+            CACHE_NUMBER: 1
           id: cache-rmgpy-env
         - name: Update environment
           run: mamba env update -n rmg_env -f RMG-Py/environment.yml
@@ -107,6 +118,7 @@ jobs:
           run: |
             cd RMG-Py
             conda activate rmg_env
+            make clean
             make
             echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
             echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
@@ -115,9 +127,7 @@ jobs:
             echo "PATH=$(pwd):$PATH" >> ~/.bashrc
             echo "export rmgpy_path=$(pwd)" >> ~/.bashrc
         
-        - name: Install PyCall RMG_ENV
-          run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-
+
         - name: Cache RMS
           id: cache-rms
           uses: actions/cache@v2
@@ -133,12 +143,10 @@ jobs:
                 ${{ runner.os }}-julia-${{ env.CACHE_NUMBER }}-rms
 
         - name: Install RMS Julia
-          run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main"));using ReactionMechanismSimulator'
+          run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master"));Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
 
-        - name: Link Python-JL
-          run: |
-            ln -sfn $(which python-jl) $(which python)
-            cd .. 
+        - name: Install PyCall RMG_ENV
+          run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
         - name: Install ARC ENV
           run: |

diff --git a/tests/test_main.py b/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)