Merge pull request #693 from ReactionMechanismGenerator/fix/failing_ci

Fix failing CI due to Python 3.9 changes

Author: JacksonBurns

.github/workflows/CI.yml

@@ -64,13 +64,13 @@ jobs:
           path: RMG-database
 
       # configures the mamba environment manager and builds the environment
-      - name: Setup Miniforge Python 3.7
+      - name: Setup Miniforge Python 3.9
         uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: RMG-Py/environment.yml
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          python-version: 3.7
+          python-version: 3.9
           activate-environment: rmg_env
           use-mamba: true
 
@@ -98,13 +98,17 @@ jobs:
           make clean
           make
 
+      - name: Setup Juliaup
+        uses: julia-actions/install-juliaup@v2
+        with:
+          channel: '1.10'
+
       # RMS installation and linking to Julia
       - name: Install and link Julia dependencies
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
-          python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
-
+          . install_rms.sh
+          
       - name: Install Q2DTor
         run: echo "" | make q2dtor
 
@@ -119,7 +123,7 @@ jobs:
         run: |
           for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat;
           do
-            if python-jl rmg.py test/regression/"$regr_test"/input.py; then
+            if python rmg.py test/regression/"$regr_test"/input.py; then
               echo "$regr_test" "Executed Successfully"
             else
               echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY
@@ -199,7 +203,7 @@ jobs:
 
             echo "<details>"
             # Compare the edge and core
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-core" \
                 $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
@@ -216,7 +220,7 @@ jobs:
             cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
             echo "<details>"
-            if python-jl scripts/checkModels.py \
+            if python scripts/checkModels.py \
                 "$regr_test-edge" \
                 $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
                 $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
@@ -237,7 +241,7 @@ jobs:
             if [ -f test/regression/"$regr_test"/regression_input.py ];
             then
               echo "<details>"
-              if python-jl rmgpy/tools/regression.py \
+              if python rmgpy/tools/regression.py \
                 test/regression/"$regr_test"/regression_input.py \
                 $REFERENCE/"$regr_test"/chemkin \
                 test/regression/"$regr_test"/chemkin