From dc73d760c86dbfe457eb637baafafdce1c465279 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Wed, 5 Apr 2023 11:25:21 -0400
Subject: [PATCH] syntax error in CI.yml, delete unused action, remove blank in
 makefile

---
 .github/workflows/CI.yml                      | 16 +--
 .../generate_regression_baseline.yml          | 99 -------------------
 Makefile                                      |  1 -
 3 files changed, 8 insertions(+), 108 deletions(-)
 delete mode 100644 .github/workflows/generate_regression_baseline.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 4f32f95716..98bbec17ca 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -72,16 +72,16 @@ jobs:
         run: make test-database
 
       # RMS installation and linking to Julia
+      # Allow these installs to 'fail' (as they do in RMG-Tests) with the command || True trick
       - name: Install and link Julia dependencies
         run: |
-        # Allow these installs to 'fail' (as they do in RMG-Tests) with the command || True trick
-          python -c "import julia;\
-           julia.install();\
-           import diffeqpy;\
-           diffeqpy.install()" || true
-          julia -e 'using Pkg;\
-           Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main"));\
-            using ReactionMechanismSimulator' || true 
+          python -c "import julia; " \
+           "julia.install(); " \
+           "import diffeqpy; " \
+           "diffeqpy.install()" || true
+          julia -e 'using Pkg; ' \
+           'Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); ' \
+           'using ReactionMechanismSimulator' || true 
           ln -sfn $(which python-jl) $(which python)
 
       # Attempt to install MOPAC
diff --git a/.github/workflows/generate_regression_baseline.yml b/.github/workflows/generate_regression_baseline.yml
deleted file mode 100644
index c3a938a62b..0000000000
--- a/.github/workflows/generate_regression_baseline.yml
+++ /dev/null
@@ -1,99 +0,0 @@
-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."
diff --git a/Makefile b/Makefile
index 2d0070fe73..0bcd4e1d81 100644
--- a/Makefile
+++ b/Makefile
@@ -85,7 +85,6 @@ eg1: all
 	coverage run rmg.py -p testing/eg1/input.py
 	coverage report
 	coverage html
-	
 eg2: all
 	mkdir -p testing/eg2
 	rm -rf testing/eg2/*