report energy in conformers_before_optimization.txt
#5380
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - main | |
| types: [opened, synchronize, reopened, ready_for_review, review_requested] | |
| schedule: | |
| - cron: '0 0 * * *' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout ARC | |
| 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-Py | |
| id: cache-rmg-py | |
| uses: actions/cache@v2 | |
| with: | |
| path: RMG-Py | |
| key: ${{ runner.os }}-rmg-main | |
| restore-keys: | | |
| ${{ runner.os }}-rmg- | |
| - name: Checkout RMG-py | |
| if: steps.cache-rmg-py.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 AutoTST | |
| id: cache-autotst | |
| uses: actions/cache@v2 | |
| with: | |
| path: AutoTST | |
| key: ${{ runner.os }}-autotst-main | |
| restore-keys: | | |
| ${{ runner.os }}-autotst- | |
| - name: Checkout AutoTST | |
| if: steps.cache-autotst.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ReactionMechanismGenerator/AutoTST | |
| path: AutoTST | |
| ref: main | |
| fetch-depth: 1 | |
| - name: Cache TS-GCN | |
| id: cache-tsgcn | |
| uses: actions/cache@v2 | |
| with: | |
| path: TS-GCN | |
| key: ${{ runner.os }}-tsgcn-main | |
| restore-keys: | | |
| ${{ runner.os }}-tsgcn- | |
| - name: Checkout TS-GCN | |
| if: steps.cache-tsgcn.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: ReactionMechanismGenerator/TS-GCN | |
| path: TS-GCN | |
| ref: main | |
| fetch-depth: 1 | |
| - name: Cache KinBot | |
| id: cache-kinbot | |
| uses: actions/cache@v2 | |
| with: | |
| path: KinBot | |
| key: ${{ runner.os }}-kinbot-2.0.6 | |
| restore-keys: | | |
| ${{ runner.os }}-kinbot- | |
| - name: Checkout Kinbot 2.0.6 | |
| if: steps.cache-kinbot.outputs.cache-hit != 'true' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: zadorlab/KinBot | |
| path: KinBot | |
| ref: v2.0.6 | |
| fetch-depth: 1 | |
| - name: Cache Packages | |
| uses: actions/cache@v2 | |
| env: | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} | |
| - name: Setup ARC Env | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: arc_env | |
| use-mamba: true | |
| - name: Cache ARC env | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.CONDA }}/envs/arc_env | |
| key: conda-${{ runner.os }}--${{ runner.arch }}-arcenv-${{ env.CACHE_NUMBER}} | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| id: cache-arc-env | |
| - name: Update environment | |
| run: mamba env update -n arc_env -f environment.yml | |
| if: steps.cache-arc-env.outputs.cache-hit != 'true' | |
| - name: Install codecov | |
| run: mamba install -y -c conda-forge codecov | |
| - name: Cythonize RMG-Py | |
| run: | | |
| cd RMG-Py | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc | |
| echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc | |
| make | |
| cd .. | |
| - name: Set ARC Path | |
| run: | | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc | |
| echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc | |
| - name: Install AutoTST | |
| run: | | |
| cd AutoTST | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc | |
| echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc | |
| mamba env create -f environment.yml | |
| # install pyaml | |
| mamba install -n tst_env -c conda-forge -y pyyaml | |
| cd .. | |
| - name: Install TS-GCN | |
| run: | | |
| cd TS-GCN | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc | |
| echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc | |
| bash devtools/create_env_cpu.sh | |
| mamba env update -n ts_gcn -f environment.yml | |
| cd .. | |
| - name: Install KinBot | |
| run: | | |
| cd KinBot | |
| conda activate arc_env | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV | |
| echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc | |
| echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc | |
| python setup.py build | |
| python setup.py install | |
| cd .. | |
| - name: Install OpenBabel | |
| run: | | |
| mamba env create -f devtools/ob_environment.yml | |
| - name: Install Sella | |
| run: | | |
| mamba env create -f devtools/sella_environment.yml | |
| - name: Install Torch Ani | |
| run: | | |
| mamba env create -f devtools/tani_environment.yml | |
| - name: Install XTB | |
| run: | | |
| mamba env create -f devtools/xtb_environment.yml | |
| - name: Test with pytest | |
| shell: bash -el {0} | |
| run: | | |
| source ~/.bashrc | |
| conda activate arc_env | |
| make test | |
| codecov --token=f259713a-7f1d-4e9c-b140-bb3bb371d3ef | |
| - name: Functional Test | |
| run: | | |
| source ~/.bashrc | |
| conda activate arc_env | |
| make test-functional | |
| # Wait ten seconds before running the next step | |
| - name: Wait | |
| run: sleep 10 | |
| - name: Code Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: f259713a-7f1d-4e9c-b140-bb3bb371d3ef | |
| file: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| verbose: true | |
| fail_ci_if_error: false |