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‎.github/workflows/CI.yml‎

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name: CI Tests
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# CI.yml
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# This file contains the script used by GitHub actions to execute the Continuous Integration (CI)
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# for RMG-Py. This includes building RMG and its dependencies, executing the unit tests,
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# functional tests, database tests, and regression tests.
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#
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# This will run automatically on any push to any branch, but will only run one instance of
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# itself at a time per branch (to avoid spawning tons of runners, which prevents them from
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# executing).
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#
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# In the regression testing section of the action the term "Stable" or "Reference" refers to
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# the 'correct answers' to the regression tests, i.e. the way that the main branch executes
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# them. These 'answers' are re-generated daily, or on any push to main, and retrieved whenever
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# a push is made to a non-main branch. The new proposed changes are referred to as "Dynamic".
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#
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# Changelog:
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# 2023-04 - Jackson Burns - Added this header, regression tests, cleanup of action in
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# in general, and documentation throughout the file.
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# 2023-05 - added Docker build steps
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# 2023-05-12 - added changes to allow running on forks
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# 2023-06-06 - added matrix build for libstdcxx-ng versions 12 and 13 on ubuntu. Only expect 12 to work.
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# 2023-06-07 - updated regression testing. Now fails if significant changes are detected.
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# 2023-06-15 - revert changes from 06-06, both now work
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name: Continuous Integration
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on:
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schedule:
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# * is a special character in YAML so you have to quote this string
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- cron: "0 8 * * *"
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# runs on all branches on both RMG-Py and forks
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push:
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# runs on PRs against RMG-Py (and anywhere else, but we add this for RMG-Py)
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pull_request:
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branches:
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- main
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types: [opened, synchronize, reopened, ready_for_review, review_requested]
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# allow calling from other repos in the ReactionMechanismGenerator organization
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workflow_call:
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# this prevents one PR from simultaneously running multiple runners, which will clog up the queue
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# and prevent other PRs from running the CI
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build-and-test-linux:
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runs-on: ubuntu-latest
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build-and-test-unix:
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strategy:
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max-parallel: 5
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env: # update this if needed to match a pull request on the RMG-database
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matrix:
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os: [ubuntu-latest, macos-latest]
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runs-on: ${{ matrix.os }}
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continue-on-error: ${{ matrix.os == 'macos-latest' }}
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# skip scheduled runs from forks
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if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
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env:
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# Update this if needed to match a pull request on the RMG-database:
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RMG_DATABASE_BRANCH: update_atom_enthalpies
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# This is true only if this is a reference case for the regression testing:
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REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && matrix.os =='ubuntu-latest' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v2
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- uses: conda-incubator/setup-miniconda@v2
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- uses: actions/checkout@v3
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# configures the mamba environment manager and builds the environment
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- name: Setup Mambaforge Python 3.7
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uses: conda-incubator/setup-miniconda@v2
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with:
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environment-file: environment.yml
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miniforge-variant: Mambaforge
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miniforge-version: latest
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python-version: 3.7
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activate-environment: rmg_env
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- name: Install codecov
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run: conda install -y -c conda-forge codecov
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- name: Conda info
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run: |
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conda info
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conda list
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- name: Install and link Julia dependencies
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run: |
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julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/ReactionMechanismGenerator/ReactionMechanismSimulator.jl\", rev=\"main\"))"
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julia -e "using Pkg; Pkg.add(\"PyCall\"); Pkg.add(\"DifferentialEquations\")"
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python -c "import julia; julia.install()"
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ln -sfn $(which python-jl) $(which python)
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- name: Install MOPAC
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env:
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MOPACKEY: ${{ secrets.MOPACKEY }}
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timeout-minutes: 1
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continue-on-error: true # allowed to fail on pull request from a forked repository
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use-mamba: true
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# list the environment for debugging purposes
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- name: mamba info
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run: |
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set +o pipefail
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yes 'Yes' | ${CONDA_PREFIX}/bin/mopac "$MOPACKEY"
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- name: Install and compile RMG
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mamba info
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mamba list
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# Clone the other needed repository
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- name: Clone RMG-Database
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run: |
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cd ..
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git clone -b $RMG_DATABASE_BRANCH https://github.com/ReactionMechanismGenerator/RMG-database.git
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cd RMG-Py
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git clone -b arkanepy3 https://github.com/mjohnson541/Q2DTor.git external/Q2DTor
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# modify env variables as directed in the RMG installation instructions
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- name: Set Environment Variables
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run: |
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RUNNER_CWD=$(pwd)
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echo "PYTHONPATH=$RUNNER_CWD/RMG-Py:$PYTHONPATH" >> $GITHUB_ENV
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echo "$RUNNER_CWD/RMG-Py" >> $GITHUB_PATH
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# RMG build step
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- name: make RMG
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run: |
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make clean
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make
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- name: Trigger RMG-tests
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if: ${{ github.event_name == 'push' && github.ref != 'refs/heads/main' && github.ref != 'refs/heads/stable' }} # only push events to branches other than main and stable
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env:
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GH_TOKEN: ${{ secrets.RMG_DEV_TOKEN }}
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run: ./trigger-rmg-tests.sh
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# RMS installation and linking to Julia
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# Allow these installs to 'fail' (as they do in RMG-Tests) with the command || True trick
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- name: Install and link Julia dependencies
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timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
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run: |
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python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" || true
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julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' || true
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# non-regression testing
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- name: Unit tests
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run: make test-unittests
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- name: Functional tests
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if: ${{ success() || failure() }} # Run even if the unit tests failed (but not if they were cancelled)
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run: make test-functional
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- name: Database tests
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if: ${{ success() || failure() }} # Run even if the functional tests failed (but not if they were cancelled)
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run: make test-database
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- name: Code coverage
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run: codecov
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# Regression Testing - Test Execution
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- name: Regression Tests - Execution
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id: regression-execution
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timeout-minutes: 60
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run: |
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for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat;
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do
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if python-jl rmg.py test/regression/"$regr_test"/input.py; then
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echo "$regr_test" "Executed Successfully"
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else
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echo "$regr_test" "Failed to Execute" | tee -a $GITHUB_STEP_SUMMARY
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export FAILED=Yes
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fi
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done
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if [[ ${FAILED} ]]; then
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echo "One or more regression tests could not be executed." | tee -a $GITHUB_STEP_SUMMARY
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echo "Please download the failed results or check the above log to see why." | tee -a $GITHUB_STEP_SUMMARY
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exit 1
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fi
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# Upload Regression Results as Failed if above step failed
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- name: Upload Failed Results
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if: ${{ failure() && steps.regression-execution.conclusion == 'failure' }}
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uses: actions/upload-artifact@v3
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with:
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name: failed regression results ${{ matrix.os }}
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path: |
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test/regression
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# Upload Regression Results as Stable if Scheduled or Push to Main
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- name: Upload Results as Reference
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# upload the results for scheduled CI (on main) and pushes to main
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if: ${{ env.REFERENCE_JOB == 'true' }}
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uses: actions/upload-artifact@v3
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with:
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name: stable_regression_results
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path: |
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test/regression
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# Upload Regression Results as Dynamic if Push to non-main Branch
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- name: Upload Results as Dynamic
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if: ${{ env.REFERENCE_JOB == 'false' }}
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uses: actions/upload-artifact@v3
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with:
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name: dynamic regression results ${{ matrix.os }}
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path: |
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test/regression
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- name: mkdir stable_regression_results
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if: ${{ env.REFERENCE_JOB == 'false' }}
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run: mkdir stable_regression_results
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# Retrieve Stable Results for reference
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# Will need to use this -> https://github.com/dawidd6/action-download-artifact
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- name: Retrieve Stable Regression Results
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if: ${{ env.REFERENCE_JOB == 'false' }}
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uses: dsnopek/action-download-artifact@91dda23aa09c68860977dd0ed11d93c0ed3795e7 # see https://github.com/ReactionMechanismGenerator/RMG-Py/pull/2459#issuecomment-1582850815
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with:
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# this will search for the last successful execution of CI on main and download
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# the stable regression results
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workflow: CI.yml
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workflow_conclusion: success
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repo: ReactionMechanismGenerator/RMG-Py
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branch: main
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name: stable_regression_results
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path: stable_regression_results
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search_artifacts: true # retrieves the last run result, either scheduled daily or on push to main
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ensure_latest: true # ensures that the latest run is retrieved
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# should result in a set of folders inside stable_regression_results
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# each of which has the stable result for that example/test
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# Regression Testing - Actual Comparisons
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- name: Regression Tests - Compare to Baseline
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id: regression-comparison
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if: ${{ env.REFERENCE_JOB == 'false' }}
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env:
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REFERENCE: stable_regression_results
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run: |
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mkdir -p "test/regression-diff"
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for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation;
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do
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echo ""
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echo "## Regression test $regr_test:"
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# Memory Usage and Execution Time
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echo -n 'Reference: '
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grep "Execution time" $REFERENCE/"$regr_test"/RMG.log | tail -1
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echo -n 'Current: '
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grep "Execution time" test/regression/"$regr_test"/RMG.log | tail -1
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echo -n 'Reference: '
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grep "Memory used:" $REFERENCE/"$regr_test"/RMG.log | tail -1
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echo -n 'Current: '
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grep "Memory used:" test/regression/"$regr_test"/RMG.log | tail -1
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# Compare the edge and core
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if python-jl scripts/checkModels.py \
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"$regr_test-core" \
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$REFERENCE/"$regr_test"/chemkin/chem_annotated.inp \
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$REFERENCE/"$regr_test"/chemkin/species_dictionary.txt \
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test/regression/"$regr_test"/chemkin/chem_annotated.inp \
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test/regression/"$regr_test"/chemkin/species_dictionary.txt
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then
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echo "$regr_test Passed Core Comparison"
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else
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echo "$regr_test Failed Core Comparison" | tee -a $GITHUB_STEP_SUMMARY
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cp "$regr_test-core.log" test/regression-diff/
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export FAILED=Yes
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fi
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if python-jl scripts/checkModels.py \
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"$regr_test-edge" \
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$REFERENCE/"$regr_test"/chemkin/chem_edge_annotated.inp \
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$REFERENCE/"$regr_test"/chemkin/species_edge_dictionary.txt \
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test/regression/"$regr_test"/chemkin/chem_edge_annotated.inp \
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test/regression/"$regr_test"/chemkin/species_edge_dictionary.txt
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then
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echo "$regr_test Passed Edge Comparison"
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else
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echo "$regr_test Failed Edge Comparison" | tee -a $GITHUB_STEP_SUMMARY
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cp "$regr_test-edge.log" test/regression-diff/
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export FAILED=Yes
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fi
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# Check for Regression between Reference and Dynamic (skip superminimal)
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if [ -f test/regression/"$regr_test"/regression_input.py ];
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then
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if python-jl rmgpy/tools/regression.py \
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test/regression/"$regr_test"/regression_input.py \
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$REFERENCE/"$regr_test"/chemkin \
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test/regression/"$regr_test"/chemkin
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then
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echo "$regr_test Passed Observable Testing"
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else
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echo "$regr_test Failed Observable Testing" | tee -a $GITHUB_STEP_SUMMARY
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export FAILED=Yes
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fi
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fi
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echo ""
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done
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if [[ ${FAILED} ]]; then
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echo "One or more regression tests failed." | tee -a $GITHUB_STEP_SUMMARY
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echo "Please download the failed results and run the tests locally or check the above log to see why." | tee -a $GITHUB_STEP_SUMMARY
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exit 1
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fi
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# Upload Regression Results as Failed if above step failed
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- name: Upload Failed Comparison Results
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if: ${{ failure() && steps.regression-comparison.conclusion == 'failure' }}
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uses: actions/upload-artifact@v3
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with:
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name: failed regression comparison results ${{ matrix.os }}
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path: |
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test/regression-diff
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# Install and Call codecov only if the tests were successful (permitting failures in the regression comparison tests)
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- name: Code coverage install and run
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if: success() || ( failure() && steps.regression-execution.conclusion == 'success' )
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run: |
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mamba install -y -c conda-forge codecov
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codecov
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build-and-push-docker:
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# after testing and on pushes to main, build and push docker image
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# technically we could live without the 'needs' since _in theory_
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# nothing will ever be merged into main that fails the tests, but
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# who knows ¯\_(ツ)_/¯
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#
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# taken from https://github.com/docker/build-push-action
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needs: build-and-test-unix
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runs-on: ubuntu-latest
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if: github.ref == 'refs/heads/main' && github.repository == 'ReactionMechanismGenerator/RMG-Py'
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steps:
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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- name: Login to Docker Hub
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Build and Push
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uses: docker/build-push-action@v4
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with:
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push: true
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tags: reactionmechanismgenerator/rmg:latest

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