CI.yml

# CI.yml
# This file contains the script used by GitHub actions to execute the Continuous Integration (CI)
# for RMG-Py. 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:
# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in
#              in general, and documentation throughout the file.
# 2023-05    - added Docker build steps
# 2023-05-12 - added changes to allow running on forks
# 2023-06-06 - added matrix build for libstdcxx-ng versions 12 and 13 on ubuntu. Only expect 12 to work.
# 2023-06-07 - updated regression testing. Now fails if significant changes are detected.
# 2023-06-15 - revert changes from 06-06, both now work
# 2023-06-27 - add option to run from RMG-database with GitHub resuable workflows
# 2023-07-17 - made it pass by default
# 2023-07-21 - upload the regression results summary as artifact (for use as a comment on PRs)
# 2023-07-31 - removed option to run from RMG-database with GitHub resuable workflows
# 2024-10-01 - deprecated Mambaforge with Miniforge3 for environment creation

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-Py (and anywhere else, but we add this for RMG-Py)
  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:
  # if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace
  # main with the name of the branch
  RMG_DATABASE_BRANCH: lithium_rebase


jobs:
  build-osx:
    runs-on: macos-13
    # skip scheduled runs from forks
    if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
    env:
      # Update this if needed to match a pull request on the RMG-database:
      RMG_DATABASE_BRANCH: lithium
      # This is true only if this is a reference case for the regression testing:
      REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && matrix.os =='ubuntu-latest' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout RMG-Py
        uses: actions/checkout@v4

      # Step to create a custom condarc.yml before setting up conda
      - name: Create custom conda config file
        run: |
          RUNNER_CWD=$(pwd)
          echo "channels:" > $RUNNER_CWD/condarc.yml
          echo "  - conda-forge" >> $RUNNER_CWD/condarc.yml
          echo "  - rmg" >> $RUNNER_CWD/condarc.yml
          echo "  - cantera" >> $RUNNER_CWD/condarc.yml
          echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml

      # configures the mamba environment manager and builds the environment
      - name: Setup Miniforge Python 3.7
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: environment.yml
          miniforge-variant: Miniforge3
          miniforge-version: latest
          python-version: 3.7
          condarc-file: condarc.yml
          activate-environment: rmg_env
          use-mamba: true

      # list the environment for debugging purposes
      - name: mamba info
        run: |
          mamba info
          mamba list

      # Clone RMG-database
      - name: Clone RMG-database
        run: |
          cd ..
          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git

      # 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-Py' && 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-Py' }}
    defaults:
      run:
        shell: bash -l {0}
    steps:
      - name: Checkout RMG-Py
        uses: actions/checkout@v4

      # Step to create a custom condarc.yml before setting up conda
      - name: Create custom condarc.yml
        run: |
          RUNNER_CWD=$(pwd)
          echo "channels:" > $RUNNER_CWD/condarc.yml
          echo "  - conda-forge" >> $RUNNER_CWD/condarc.yml
          echo "  - rmg" >> $RUNNER_CWD/condarc.yml
          echo "  - cantera" >> $RUNNER_CWD/condarc.yml
          echo "show_channel_urls: true" >> $RUNNER_CWD/condarc.yml

      # configures the mamba environment manager and builds the environment
      - name: Setup Miniforge Python 3.7
        uses: conda-incubator/setup-miniconda@v3
        with:
          environment-file: environment.yml
          miniforge-variant: Miniforge3
          miniforge-version: latest
          python-version: 3.7
          condarc-file: condarc.yml
          activate-environment: rmg_env
          use-mamba: true

      # list the environment for debugging purposes
      - name: mamba info
        run: |
          mamba info
          mamba list

      # Clone RMG-database
      - name: Clone RMG-database
        run: |
          cd ..
          git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git

      # 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="marcus_development")); using ReactionMechanismSimulator'

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

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

      # 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 RMS_constantVIdealGasReactor_fragment minimal_surface;
          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@v4
        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@v4
        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@v4
        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
      - name : Find ID of Reference Results
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        # this will search for the last successful execution of CI on main
        run: |
          run_id=$(gh run list -R ReactionMechanismGenerator/RMG-Py --workflow="Continuous Integration" --branch main --limit 15 --json databaseId,conclusion --jq 'map(select(.conclusion == "success")) | .[0].databaseId')
          echo "CI_RUN_ID=$run_id" >> $GITHUB_ENV

      - name: Retrieve Stable Regression Results
        if: ${{ env.REFERENCE_JOB == 'false' }}
        uses: actions/download-artifact@v4
        with:
        # download stable regression results
          run-id: ${{ env.CI_RUN_ID }}
          repository: ReactionMechanismGenerator/RMG-Py
          github-token: ${{ secrets.GITHUB_TOKEN }}
          name: stable_regression_results
          path: stable_regression_results

      # 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 fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
          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 "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
            echo "</details>"
            echo "<details>"
            if python-jl scripts/checkModels.py \
                "$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 "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>"

            # 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

      # Install and Call codecov only if the tests were successful (permitting failures in the regression comparison tests)
      - name: Code coverage install and run
        if: success() || ( failure() && steps.regression-execution.conclusion == 'success' )
        run: |
          mamba install -y -c conda-forge codecov
          codecov

  build-and-push-docker:
    # after testing and on pushes to main, build and push docker image
    # technically we could live without the 'needs' since _in theory_
    # nothing will ever be merged into main that fails the tests, but
    # who knows ¯\_(ツ)_/¯
    #
    # taken from https://github.com/docker/build-push-action
    needs: build-and-test-linux
    runs-on: ubuntu-latest
    if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
    steps:
      - name: Set up QEMU
        uses: docker/setup-qemu-action@v2

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2

      - name: Login to Docker Hub
        uses: docker/login-action@v2
        with:
          username: ${{ secrets.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_TOKEN }}

      - name: Build and Push
        uses: docker/build-push-action@v4
        with:
          push: true
          tags: reactionmechanismgenerator/rmg:latest