Continuous Integration #536
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 | |
| 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: main | |
| jobs: | |
| build-osx: | |
| runs-on: macos-latest | |
| # skip scheduled runs from forks | |
| if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout RMG-Py | |
| uses: actions/checkout@v4 | |
| # configures the mamba environment manager and builds the environment | |
| - 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 | |
| # 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 | |
| # configures the mamba environment manager and builds the environment | |
| - 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 | |
| # 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" >> $GITHUB_PATH | |
| # RMG build step | |
| - name: make RMG | |
| run: | | |
| make clean | |
| make | |
| # RMS installation and linking to Julia | |
| - name: Install and link Julia dependencies | |
| timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours). | |
| run: | | |
| python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" | |
| julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' | |
| - name: Install Q2DTor | |
| run: echo "" | make q2dtor | |
| # non-regression testing | |
| - name: Run Unit, Functional, and Database Tests | |
| # aggregate into one command so we only have to eat the collection time once | |
| run: make test-all | |
| # Regression Testing - Test Execution | |
| - name: Regression Tests - Execution | |
| id: regression-execution | |
| timeout-minutes: 60 | |
| run: | | |
| for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment; | |
| do | |
| if python-jl rmg.py test/regression/"$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-Py | |
| 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 fragment RMS_constantVIdealGasReactor_fragment; | |
| 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 | |
| # 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 |