CI.yml

# CI.yml
# This file contains the script used by GitHub actions to execute the Continuous Integration (CI)
# for RMG-database. This includes building RMG and its dependencies, executing the unit tests,
# functional tests, database tests, and regression tests.
# 
# This will run automatically on any push to any branch, but will only run one instance of
# itself at a time per branch (to avoid spawning tons of runners, which prevents them from
# executing).
#
# In the regression testing section of the action the term "Stable" or "Reference" refers to
# the 'correct answers' to the regression tests, i.e. the way that the main branch executes
# them. These 'answers' are re-generated daily, or on any push to main, and retrieved whenever
# a push is made to a non-main branch. The new proposed changes are referred to as "Dynamic".
#
#
# Changelog:
# 2023-10    - Copied from RMG-Py, adapted for RMG-database

name: Continuous Integration

on:
  schedule:
    # * is a special character in YAML so you have to quote this string
    - cron: "0 8 * * *"
  # runs on all branches on both RMG-Py and forks
  push:
  # runs on PRs against RMG-database (and anywhere else, but we add this for RMG-database
  pull_request:

# this prevents one PR from simultaneously running multiple runners, which will clog up the queue
# and prevent other PRs from running the CI
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

env:
  # update this to run tests with un merged rmg-py branches
  RMG_PY_BRANCH: main

jobs:
  build-osx:
    runs-on: macos-latest
    # skip scheduled runs from forks
    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-database' && github.event_name == 'schedule' ) }}
    defaults:
      run:
        shell: bash -l {0}
        working-directory: RMG-Py
    steps:
      - name: Clone RMG-database
        uses: actions/checkout@v3
        with:
          path: RMG-database

      - name: Checkout RMG-Py
        uses: actions/checkout@v3
        with:
          path: RMG-Py
          repository: ReactionMechanismGenerator/RMG-Py
          ref: ${{ env.RMG_PY_BRANCH }}

      # configures the mamba environment manager and builds the environment
      - name: Setup Mambaforge Python 3.7
        uses: conda-incubator/setup-miniconda@v2
        with:
          environment-file: RMG-Py/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

      # modify env variables as directed in the RMG installation instructions
      - name: Set Environment Variables
        run: |
          RUNNER_CWD=$(pwd)
          echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
          echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH

      # RMG build step
      - name: make RMG
        run: |
          make clean
          make

  build-and-test-linux:
    runs-on: ubuntu-latest
    # skip scheduled runs from forks
    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-database' && github.event_name == 'schedule' ) }}
    env: 
      # This is true only if this is a reference case for the regression testing:
      REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-database' }}
    defaults:
      run:
        shell: bash -l {0}
        working-directory: RMG-Py
    steps:
      - name: Clone RMG-database
        uses: actions/checkout@v3
        with:
          path: RMG-database

      - name: Checkout RMG-Py
        uses: actions/checkout@v3
        with:
          path: RMG-Py
          repository: ReactionMechanismGenerator/RMG-Py
          ref: ${{ env.RMG_PY_BRANCH }}

      # configures the mamba environment manager and builds the environment
      - name: Setup Mambaforge Python 3.7
        uses: conda-incubator/setup-miniconda@v2
        with:
          environment-file: RMG-Py/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

      # modify env variables as directed in the RMG installation instructions
      - name: Set Environment Variables
        run: |
          RUNNER_CWD=$(pwd)
          echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
          echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH

      # RMG build step
      - name: make RMG
        run: |
          make clean
          make

      # 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="main")); using ReactionMechanismSimulator'

      - name: Install Q2DTor
        run: echo "" | make q2dtor

      # non-regression testing
      - name: Run Database Tests
        # aggregate into one command so we only have to eat the collection time once
        run: make test-database

      # Regression Testing - Test Execution
      - name: Regression Tests - Execution
        id: regression-execution
        timeout-minutes: 60
        run: |
          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment;
          do
            if python-jl 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
              export FAILED=Yes
            fi
          done
          if [[ ${FAILED} ]]; then
            echo "One or more regression tests could not be executed." | tee -a $GITHUB_STEP_SUMMARY
            echo "Please download the failed results or check the above log to see why." | tee -a $GITHUB_STEP_SUMMARY
            exit 1
          fi

      # Upload Regression Results as Failed if above step failed
      - name: Upload Failed Results
        if: ${{ failure() && steps.regression-execution.conclusion == 'failure' }}
        uses: actions/upload-artifact@v3
        with:
          name: failed_regression_results
          path: |
            test/regression

      # Upload Regression Results as Stable if Scheduled or Push to Main
      - name: Upload Results as Reference
        # upload the results for scheduled CI (on main) and pushes to main
        if: ${{ env.REFERENCE_JOB == 'true' }}
        uses: actions/upload-artifact@v3
        with:
          name: stable_regression_results
          path: |
            test/regression

      # Upload Regression Results as Dynamic if Push to non-main Branch
      - name: Upload Results as Dynamic
        if: ${{ env.REFERENCE_JOB == 'false' }}
        uses: actions/upload-artifact@v3
        with:
          name: dynamic_regression_results
          path: |
            test/regression

      - name: mkdir stable_regression_results
        if: ${{ env.REFERENCE_JOB == 'false' }}
        run: mkdir stable_regression_results

      # Retrieve Stable Results for reference
      # Will need to use this -> https://github.com/dawidd6/action-download-artifact
      - name: Retrieve Stable Regression Results
        if: ${{ env.REFERENCE_JOB == 'false' }}
        uses: dsnopek/action-download-artifact@91dda23aa09c68860977dd0ed11d93c0ed3795e7 # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2459#issuecomment-1582850815
        with:
        # this will search for the last successful execution of CI on main and download
        # the stable regression results
          workflow: CI.yml
          workflow_conclusion: success
          repo: ReactionMechanismGenerator/RMG-database
          branch: main
          name: stable_regression_results
          path: stable_regression_results
          search_artifacts: true  # retrieves the last run result, either scheduled daily or on push to main
          ensure_latest: true     # ensures that the latest run is retrieved
          # should result in a set of folders inside stable_regression_results
          # each of which has the stable result for that example/test

      # Regression Testing - Actual Comparisons
      - name: Regression Tests - Compare to Baseline
        id: regression-comparison
        if: ${{ env.REFERENCE_JOB == 'false' }}
        env:
          REFERENCE: stable_regression_results
        run: |
          exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
          mkdir -p "test/regression-diff"
          for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation;
          do
            echo ""
            echo "### Regression test $regr_test:"
            # Memory Usage and Execution Time
            echo -n 'Reference: '
            grep "Execution time" $REFERENCE/"$regr_test"/RMG.log | tail -1
            echo -n 'Current:   '
            grep "Execution time" test/regression/"$regr_test"/RMG.log | tail -1
            echo -n 'Reference: '
            grep "Memory used:" $REFERENCE/"$regr_test"/RMG.log | tail -1
            echo -n 'Current:   '
            grep "Memory used:" test/regression/"$regr_test"/RMG.log | tail -1

            echo "<details>"
            # Compare the edge and core
            if python-jl scripts/checkModels.py \
                "$regr_test-core" \
                $REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
                $REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
                test/regression/"$regr_test"/chemkin/chem_annotated.inp \
                test/regression/"$regr_test"/chemkin/species_dictionary.txt
            then
              echo "<summary>$regr_test Passed Core Comparison ✅</summary>"
            else
              echo "<summary>$regr_test Failed Core Comparison ❌</summary>"
              cp "$regr_test-core.log" test/regression-diff/
              export FAILED=Yes
            fi
            echo "" # blank line so next block is interpreted as markdown
            cat "$regr_test-core.log"
            echo "</details>"
            echo "<details>"
            if python-jl scripts/checkModels.py \
                "$regr_test-edge" \
                $REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
                $REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
                test/regression/"$regr_test"/chemkin/chem_edge_annotated.inp \
                test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt
            then
              echo "<summary>$regr_test Passed Edge Comparison ✅</summary>"
            else
              echo "<summary>$regr_test Failed Edge Comparison ❌</summary>"
              cp "$regr_test-edge.log" test/regression-diff/
              export FAILED=Yes
            fi
            echo "" # blank line so next block is interpreted as markdown
            cat "$regr_test-edge.log"
            echo "</details>"

            # Check for Regression between Reference and Dynamic (skip superminimal)
            if [ -f test/regression/"$regr_test"/regression_input.py ];
            then
              echo "<details>"
              if python-jl rmgpy/tools/regression.py \
                test/regression/"$regr_test"/regression_input.py \
                $REFERENCE/"$regr_test"/chemkin \
                test/regression/"$regr_test"/chemkin
              then
                echo "<summary>$regr_test Passed Observable Testing ✅</summary>"
              else
                echo "<summary>$regr_test Failed Observable Testing ❌</summary>"
                export FAILED=Yes
              fi
              echo "</details>"
            fi
            echo ""
          done
          if [[ ${FAILED} ]]; then
            echo "⚠️ One or more regression tests failed." | tee -a $GITHUB_STEP_SUMMARY >&2
            echo "Please download the failed results and run the tests locally or check the log to see why." | tee -a $GITHUB_STEP_SUMMARY >&2
          fi

      - name: Prepare Results for PR Comment
        if: ${{ env.REFERENCE_JOB == 'false' }}
        env:
          PR_NUMBER: ${{ github.event.number || github.event.after || github.event_name }}
        run: |
          echo $PR_NUMBER > summary.txt
          echo "## Regression Testing Results" >> summary.txt
          cat regression.stderr >> summary.txt
          echo "<details>" >> summary.txt
          echo "<summary>Detailed regression test results.</summary>" >> summary.txt
          cat regression.stdout >> summary.txt
          echo "</details>" >> summary.txt
          echo "" >> summary.txt
          echo "_beep boop this comment was written by a bot_ :robot:" >> summary.txt
          cat summary.txt > $GITHUB_STEP_SUMMARY

      - name: Upload regression summary artifact
       # the annotate workflow uses this artifact to add a comment to the PR
        uses: actions/upload-artifact@v3
        if : ${{ github.event_name == 'pull_request' }}
        with:
          name: regression_summary
          path: summary.txt

      - name: Upload Comparison Results
        uses: actions/upload-artifact@v3
        with:
          name: regression_test_comparison_results
          path: |
            test/regression-diff