Lithium rebase #2056
Workflow file for this run
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-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 | |
| # 2024/10/02 Mambaforge is deprecated. Use Miniforge3 instead. | |
| 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-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 # only applies to 'run' steps | |
| steps: | |
| - name: Checkout RMG-Py | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: ReactionMechanismGenerator/RMG-Py | |
| ref: ${{ env.RMG_PY_BRANCH }} | |
| path: RMG-Py | |
| - name: Checkout RMG-database | |
| uses: actions/checkout@v4 | |
| with: | |
| path: RMG-database | |
| # configures the mamba environment manager and builds the environment | |
| - name: Setup Miniforge Python 3.7 | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: RMG-Py/environment.yml | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| python-version: 3.7 | |
| activate-environment: rmg_env | |
| use-mamba: true | |
| # list the environment for debugging purposes | |
| - name: mamba info | |
| run: | | |
| mamba info | |
| mamba list | |
| # modify env variables as directed in the RMG installation instructions | |
| - name: Set Environment Variables | |
| run: | | |
| RUNNER_CWD=$(pwd) | |
| echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV | |
| echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH | |
| # RMG build step | |
| - name: make RMG | |
| run: | | |
| make clean | |
| make | |
| # RMS installation and linking to Julia | |
| - name: Install and link Julia dependencies | |
| timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours). | |
| run: | | |
| python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" | |
| julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator' | |
| - name: Install Q2DTor | |
| run: echo "" | make q2dtor | |
| # non-regression testing | |
| - name: Run Database Tests | |
| run: make test-database | |
| # Regression Testing - Test Execution | |
| - name: Regression Tests - Execution | |
| id: regression-execution | |
| timeout-minutes: 60 | |
| run: | | |
| for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat; | |
| do | |
| if python-jl rmg.py test/regression/"$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: | | |
| RMG-Py/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: | | |
| RMG-Py/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: RMG-Py/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; | |
| 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: RMG-Py/summary.txt | |
| - name: Upload Comparison Results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: regression_test_comparison_results | |
| path: | | |
| RMG-Py/test/regression-diff |