change workflow to run on main #486
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| name: test | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| # First, check if the types/formatting is correct. | |
| types-and-linting: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| architecture: x64 | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 black mypy | |
| python -m pip install -r requirements.txt | |
| - name: Lint with Black | |
| uses: rickstaa/action-black@v1 | |
| with: | |
| black_args: ". --check" | |
| - name: Check types | |
| run: | | |
| mypy biobalm | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 biobalm --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 biobalm --ignore=E203,W503,C901 --select=C,E,F,W,B,B950 --max-line-length=127 --statistics --count --max-complexity=10 | |
| doctests: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 5 | |
| needs: [types-and-linting] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install clingo | |
| run: sudo apt-get -y install gringo | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| architecture: x64 | |
| - name: Fetch and install native Pint | |
| run: | | |
| wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb | |
| sudo apt install ./pint_2019-05-24_amd64.deb | |
| - name: Fetch and install Mole | |
| run: | | |
| wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz | |
| tar -xvf mole-140428.tar.gz | |
| (cd ./mole-140428 && make) | |
| (cd ./mole-140428 && pwd >> $GITHUB_PATH) | |
| - name: Install repo dependencies | |
| run: pip install -r requirements.txt | |
| - name: Run doctests | |
| run: python -m doctest biobalm/*.py | |
| # Then do a "small" test run with code coverage. | |
| coverage: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| needs: [types-and-linting, doctests] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install clingo | |
| run: sudo apt-get -y install gringo | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| architecture: x64 | |
| - name: Fetch and install native Pint | |
| run: | | |
| wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb | |
| sudo apt install ./pint_2019-05-24_amd64.deb | |
| - name: Fetch and install Mole | |
| run: | | |
| wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz | |
| tar -xvf mole-140428.tar.gz | |
| (cd ./mole-140428 && make) | |
| (cd ./mole-140428 && pwd >> $GITHUB_PATH) | |
| - name: Install repo dependencies | |
| run: pip install -r requirements.txt | |
| - name: Install pytest | |
| run: pip install pytest pytest-cov | |
| - name: Run pytest with coverage | |
| run: python3 -m pytest --networksize 20 --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=biobalm tests/ | tee pytest-coverage.txt | |
| - name: Pytest coverage comment | |
| uses: MishaKav/pytest-coverage-comment@main | |
| with: | |
| pytest-coverage-path: ./pytest-coverage.txt | |
| junitxml-path: ./pytest.xml | |
| # Then do a full test for correctness using larger networks. | |
| tests: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| needs: [types-and-linting, doctests, coverage] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Install clingo | |
| run: sudo apt-get -y install gringo | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| architecture: x64 | |
| - name: Fetch and install native Pint | |
| run: | | |
| wget https://github.com/pauleve/pint/releases/download//2019-05-24/pint_2019-05-24_amd64.deb | |
| sudo apt install ./pint_2019-05-24_amd64.deb | |
| - name: Fetch and install Mole | |
| run: | | |
| wget http://www.lsv.fr/~schwoon/tools/mole/mole-140428.tar.gz | |
| tar -xvf mole-140428.tar.gz | |
| (cd ./mole-140428 && make) | |
| (cd ./mole-140428 && pwd >> $GITHUB_PATH) | |
| - name: Install repo dependencies | |
| run: pip install -r requirements.txt | |
| - name: Install pytest | |
| run: pip install pytest | |
| - name: Run pytest (without coverage) | |
| run: python3 -m pytest --networksize 30 tests/ |