minimum example to test formatting and feasibility

.github/workflows/CI.yml

@@ -60,7 +60,7 @@ jobs:
           yes 'Yes' | ${CONDA_PREFIX}/bin/mopac "$MOPACKEY"
 
       # Clone the other needed repositories
-      - name: Install and compile RMG
+      - name: Install and Compile RMG
         run: |
           cd ..
           git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
@@ -78,12 +78,43 @@ jobs:
         if: ${{ success() || failure() }} # Run even if the functional tests failed (but not if they were cancelled)
         run: make test-database
 
+      # Retrieve Stable Results for reference
+      - name: Retrieve Stable Regression Results
+        run: |
+          echo "Jackson, implement this."
+          # should result in a set of folders, each of which has the stable result for that example/test
+
       # Regression Testing
       - name: Regression Tests
-        if: ${{ github.event_name == 'push' && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/stable' }} # only push events to branches other than main and stable
-        env:
-          GH_TOKEN: ${{ secrets.RMG_DEV_TOKEN }}
-        run: ./trigger-rmg-tests.sh
+        run: |
+          timeout 600 python-jl rmg.py test/regression/aromatics/input.py
+          # python-jl scripts/checkModels.py test/regression/aromatics $benchmark_model/chemkin/chem_annotated.inp $benchmark_model/chemkin/species_dictionary.txt $testing_model/chemkin/chem_annotated.inp $testing_model/chemkin/species_dictionary.txt
+          # aromatics_status=$?
+          # ./run.sh test/regression/nitrogen
+          # nitrogen_status=$?
+          # ./run.sh test/regression/sulfur
+          # sulfur_status=$?
+          # ./run.sh test/regression/oxidation
+          # oxidation_status=$?
+          # ./run.sh test/regression/liquid_oxidation
+          # liquid_oxidation_status=$?
+          # ./run.sh test/regression/superminimal
+          # superminimal_status=$?
+          # ./run.sh test/regression/eg1
+          # eg1_status=$?
+
+          # echo "aromatics status: $aromatics_status"
+          # echo "nitrogen status: $nitrogen_status"
+          # echo "sulfur status: $sulfur_status"
+          # echo "oxidation status: $oxidation_status"
+          # echo "liquid oxidation status: $liquid_oxidation_status"
+          # echo "superminimal status: $superminimal_status"
+          # echo "eg1 status: $eg1_status"
+          # if [ $(($aromatics_status | $nitrogen_status | $sulfur_status | $oxidation_status | $liquid_oxidation_status | $superminimal_status | $eg1_status)) -ne 0 ];
+          # then
+          #   echo "Failed regression tests (non-zero exit code from regression test)"
+          #   exit 1
+          # fi
 
       # Install and Call codecov only if ALL the tests were successful
       - name: Code coverage install and run

.github/workflows/generate_regression_baseline.yml

@@ -0,0 +1,99 @@
+name: Generate Regression Baseline
+
+on:
+  workflow_dispatch:
+
+  schedule:
+    - cron: "0 6 * * 1-5"
+
+jobs:
+  build-and-test-linux:
+    runs-on: ubuntu-latest
+    env: # update this if needed to match a pull request on the RMG-database
+      RMG_DATABASE_BRANCH: main
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+
+      # configures the mamba environment manager
+      - name: Setup Mambaforge Python 3.7
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          python-version: 3.7
+          activate-environment: rmg_env
+          use-mamba: true
+
+      # list the environment for debugging purposes
+      - name: mamba info
+        run: |
+          mamba info
+          mamba list
+
+      # RMG installation and linking to Julia
+      - name: Install and link Julia dependencies
+        run: |
+          julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
+          julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
+          python -c "import julia; julia.install()"
+          ln -sfn $(which python-jl) $(which python)
+
+      # Attempt to install MOPAC
+      - name: Install MOPAC
+        env:
+          MOPACKEY: ${{ secrets.MOPACKEY }}
+        timeout-minutes: 1
+        continue-on-error: true # allowed to fail on pull request from a forked repository
+        run: |
+          set +o pipefail
+          yes 'Yes' | ${CONDA_PREFIX}/bin/mopac "$MOPACKEY"
+
+      # Clone the other needed repositories
+      - name: Install and Compile RMG
+        run: |
+          cd ..
+          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
+          cd RMG-Py
+          git clone -b arkanepy3 https://github.com/mjohnson541/Q2DTor.git external/Q2DTor
+          make
+
+      # Regression Testing
+      - name: Regression Tests
+        run: |
+          timeout 600 python-jl rmg.py test/regression/aromatics/input.py
+          # python-jl scripts/checkModels.py test/regression/aromatics $benchmark_model/chemkin/chem_annotated.inp $benchmark_model/chemkin/species_dictionary.txt $testing_model/chemkin/chem_annotated.inp $testing_model/chemkin/species_dictionary.txt
+          # aromatics_status=$?
+          # ./run.sh test/regression/nitrogen
+          # nitrogen_status=$?
+          # ./run.sh test/regression/sulfur
+          # sulfur_status=$?
+          # ./run.sh test/regression/oxidation
+          # oxidation_status=$?
+          # ./run.sh test/regression/liquid_oxidation
+          # liquid_oxidation_status=$?
+          # ./run.sh test/regression/superminimal
+          # superminimal_status=$?
+          # ./run.sh test/regression/eg1
+          # eg1_status=$?
+
+          # echo "aromatics status: $aromatics_status"
+          # echo "nitrogen status: $nitrogen_status"
+          # echo "sulfur status: $sulfur_status"
+          # echo "oxidation status: $oxidation_status"
+          # echo "liquid oxidation status: $liquid_oxidation_status"
+          # echo "superminimal status: $superminimal_status"
+          # echo "eg1 status: $eg1_status"
+          # if [ $(($aromatics_status | $nitrogen_status | $sulfur_status | $oxidation_status | $liquid_oxidation_status | $superminimal_status | $eg1_status)) -ne 0 ];
+          # then
+          #   echo "Failed regression tests (non-zero exit code from regression test)"
+          #   exit 1
+          # fi
+
+      # Install and Call codecov only if ALL the tests were successful
+      - name: Upload Results as Artifacts
+        run: |
+          echo "Jackson do this also."