Add an option to set time limit for route extraction (#104) #545
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| name: CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: | |
| jobs: | |
| test-core: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.7", "3.9"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: test-core (Python ${{ matrix.python-version }}) | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: environment.yml | |
| - name: Install syntheseus | |
| run: | | |
| pip install .[dev] | |
| - name: Run pre-commit | |
| run: | | |
| pre-commit run --verbose --all-files | |
| - name: Run unit tests | |
| run: | | |
| coverage run -p -m pytest ./syntheseus/tests/ | |
| coverage report --data-file .coverage.* | |
| - name: Upload coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: .coverage.core-${{ matrix.python-version }} | |
| path: .coverage.* | |
| include-hidden-files: true | |
| test-models: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| name: test-models | |
| steps: | |
| - name: Free extra disk space | |
| uses: jlumbroso/free-disk-space@main | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| environment-file: environment_full.yml | |
| - name: Install syntheseus with all single-step models | |
| run: | | |
| sudo apt install graphviz | |
| pip install .[all] | |
| - name: Run single-step model tests | |
| run: | | |
| coverage run -p -m pytest \ | |
| ./syntheseus/tests/cli/test_cli.py \ | |
| ./syntheseus/tests/reaction_prediction/inference/test_models.py \ | |
| ./syntheseus/tests/reaction_prediction/utils/test_parallel.py | |
| coverage report --data-file .coverage.* | |
| - name: Upload coverage report | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: .coverage.models | |
| path: .coverage.* | |
| include-hidden-files: true | |
| coverage: | |
| needs: [test-core, test-models] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install coverage | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| merge-multiple: true | |
| - name: Generate a combined coverage report | |
| run: | | |
| coverage combine | |
| coverage report |