[Python 3.9] Clar SciPy Re-implementation, pythoncall Debugging, Optional RMS
#5012
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| # 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 * * *" | |
| # allow running on RMG-Py on a pushed branch, only if triggered manually | |
| workflow_dispatch: | |
| # 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-and-test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9"] | |
| os: [macos-13, macos-latest, ubuntu-latest] | |
| test_julia: [yes, no] | |
| runs-on: ${{ matrix.os }} | |
| name: ${{ matrix.os }} Build and Test Python ${{ matrix.python-version }} (Julia? ${{ matrix.test_julia }}) | |
| # 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 Mambaforge Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| environment-file: environment.yml | |
| miniforge-variant: Miniforge3 | |
| miniforge-version: latest | |
| python-version: ${{ matrix.python-version }} | |
| 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" >> $GITHUB_PATH | |
| # RMG build step | |
| - name: make RMG | |
| run: | | |
| make clean | |
| make | |
| # Setup Juliaup | |
| - name: Set Julia paths | |
| if: matrix.test_julia == 'yes' | |
| run: | | |
| # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV | |
| # echo "JULIAUP_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH | |
| # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_ENV | |
| # echo "JULIA_DEPOT_PATH=$CONDA/envs/rmg_env/.julia" >> $GITHUB_PATH | |
| # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV | |
| # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH | |
| # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_ENV | |
| # echo "JULIA_CONDAPKG_EXE=$CONDA/condabin/mamba" >> $GITHUB_PATH | |
| echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_ENV | |
| # echo "JULIA_CONDAPKG_BACKEND=Current" >> $GITHUB_PATH | |
| - name: Setup Juliaup | |
| if: matrix.test_julia == 'yes' | |
| uses: julia-actions/install-juliaup@v2 | |
| with: | |
| channel: '1.9' | |
| - name: Check Julia version | |
| if: matrix.test_julia == 'yes' | |
| run: julia --version | |
| # RMS installation and linking to Julia | |
| - name: Install and link Julia dependencies | |
| if: matrix.test_julia == 'yes' | |
| timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours). | |
| # JULIA_CONDAPKG_EXE points to the existing conda/mamba to avoid JuliaCall from installing their own. See https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#If-you-already-have-a-Conda-environment. | |
| run: | | |
| mamba install conda-forge::pyjuliacall | |
| julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(name="ReactionMechanismSimulator", url="https://github.com/hwpang/ReactionMechanismSimulator.jl.git", rev="fix_installation")); using ReactionMechanismSimulator' | |
| - name: Install Q2DTor | |
| run: echo "" | make q2dtor | |
| # non-regression testing | |
| - name: Run Unit, Functional, and Database Tests | |
| # aggregate into one command so we only have to eat the collection time once | |
| run: make test-all | |
| # Regression Testing - Test Execution | |
| - name: Regression Tests - Execution | |
| id: regression-execution | |
| timeout-minutes: 60 | |
| run: | | |
| for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface; | |
| do | |
| if python rmg.py test/regression/"$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/"$regr_test"/RMG.log | tail -1 | |
| echo "<details>" | |
| # Compare the edge and core | |
| if python scripts/checkModels.py \ | |
| "$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 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/"$regr_test"/regression_input.py ]; | |
| then | |
| echo "<details>" | |
| if python rmgpy/tools/regression.py \ | |
| test/regression/"$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 | |
| 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@v6 | |
| with: | |
| push: true | |
| tags: reactionmechanismgenerator/rmg:latest |