Merge branch 'feat/py39' of https://github.com/ReactionMechanismGenerator/RMG-Py into feat/py39

Author: JacksonBurns

.github/workflows/CI.yml

@@ -81,6 +81,16 @@ jobs:
           activate-environment: rmg_env
           use-mamba: true
 
+      - name: Fix ARM Mac environment
+        if: matrix.os == 'macos-latest'
+        run: |
+          conda deactivate
+          conda env remove -n rmg_env
+          conda create -n rmg_env
+          conda activate rmg_env
+          conda config --env --set subdir osx-64
+          conda env update -f environment.yml
+
       # list the environment for debugging purposes
       - name: mamba info
         run: |
@@ -107,9 +117,18 @@ jobs:
           make
 
       # Setup Juliaup
-      - name: Set JULIAUP_DEPOT_PATH
+      - name: Set Julia paths
         run: |
           echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV
+          echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH
+          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV
+          echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH
 
       - name: Setup Juliaup
         uses: julia-actions/install-juliaup@v2
@@ -124,8 +143,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment.
         run: |
-          export JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba
-          julia -e 'ENV["JULIA_CONDAPKG_BACKEND"] = "Current"; using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor