Fix species identification in reaction wells when generating flux diagrams #941
Workflow file for this run
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| name: CI | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| types: [opened, synchronize, reopened, ready_for_review, review_requested] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout T3 | |
| uses: actions/checkout@v3 | |
| - name: Clean Ubuntu Image | |
| uses: kfir4444/free-disk-space@main | |
| with: | |
| # This may remove tools actually needed - currently does not | |
| tool-cache: true | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| swap-storage: true | |
| - name: Cache RMG | |
| id: cache-rmg | |
| uses: actions/cache@v2 | |
| with: | |
| path: RMG-Py | |
| key: ${{ runner.os }}-rmg-main | |
| restore-keys: | | |
| ${{ runner.os }}-rmg- | |
| - name: Debug RMG Cache | |
| run: | | |
| echo "cache hit: ${{ steps.cache-rmg.outputs.cache-hit }}" | |
| - name: Checkout RMG | |
| if: steps.cache-rmg.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ReactionMechanismGenerator/RMG-Py | |
| path: RMG-Py | |
| ref: main | |
| fetch-depth: 1 | |
| - name: Cache RMG-database | |
| id: cache-rmg-db | |
| uses: actions/cache@v2 | |
| with: | |
| path: RMG-database | |
| key: ${{ runner.os }}-rmgdb-main | |
| restore-keys: | | |
| ${{ runner.os }}-rmgdb- | |
| - name: Checkout RMG-database | |
| if: steps.cache-rmg-db.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ReactionMechanismGenerator/RMG-database | |
| path: RMG-database | |
| ref: main | |
| fetch-depth: 1 | |
| - name: Cache ARC | |
| id: cache-arc | |
| uses: actions/cache@v2 | |
| with: | |
| path: ARC | |
| key: ${{ runner.os }}-arc-main | |
| restore-keys: | | |
| ${{ runner.os }}-arc- | |
| - name: Checkout ARC | |
| if: steps.cache-arc.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ReactionMechanismGenerator/ARC | |
| path: ARC | |
| ref: main | |
| fetch-depth: 1 | |
| - name: Cache Conda Packages | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}-t3 | |
| - name: Setup RMG-Py Env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: rmg_env | |
| use-mamba: true | |
| - name: Cache RMG-Py env | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.CONDA }}/envs/rmg_env | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}-rmgpyenv-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 1 | |
| id: cache-rmgpy-env | |
| - name: Update environment | |
| run: mamba env update -n rmg_env -f RMG-Py/environment.yml | |
| if: steps.cache-rmgpy-env.outputs.cache-hit != 'true' | |
| - name: Cythonize RMG-Py | |
| run: | | |
| cd RMG-Py | |
| conda activate rmg_env | |
| make clean | |
| make | |
| echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV | |
| echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV | |
| echo "export rmgpy_path=$(pwd)" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc | |
| echo "PATH=$(pwd):$PATH" >> ~/.bashrc | |
| echo "export rmgpy_path=$(pwd)" >> ~/.bashrc | |
| - name: Install RMS Julia | |
| run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master"));Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;' | |
| - name: Install PyCall RMG_ENV | |
| run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" | |
| - name: Install ARC ENV | |
| run: | | |
| cd ARC | |
| mamba env create -f environment.yml | |
| conda activate arc_env | |
| echo "export arc_path=$(pwd)" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV | |
| echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV | |
| echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> ~/.bashrc | |
| echo "PATH=$(pwd):$PATH" >> ~/.bashrc | |
| echo "export arc_path=$(pwd)" >> ~/.bashrc | |
| cd .. | |
| - name: Install xtb | |
| run: | | |
| mamba create -n xtb_env python=3.7 -c conda-forge -y | |
| conda activate xtb_env | |
| mamba install -c conda-forge xtb=6.3.3 -y | |
| mamba install -c anaconda pyyaml -y | |
| - name: Install T3 | |
| run: | | |
| mamba env create -f environment.yml | |
| - name: Install CodeCov | |
| run: | | |
| conda activate t3_env | |
| mamba install -c conda-forge codecov | |
| mamba install -c conda-forge pytest-cov | |
| - name: Run T3 Tests | |
| shell: bash -el {0} | |
| run: | | |
| source ~/.bashrc | |
| conda activate t3_env | |
| make test | |
| codecov --token=${{ secrets.CODECOV_TOKEN }} | |
| - name: Code Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| verbose: true | |
| fail_ci_if_error: true |