Minor bug fixes #957
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| name: CI | |
| # trigger | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| schedule: | |
| # run Monday and Thursday at 03:18 UTC | |
| - cron: '18 15 * * MON,THU' | |
| jobs: | |
| base: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.10'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-base | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh base R | |
| - name: Run tests | |
| timeout-minutes: 15 | |
| run: tox -e base | |
| - name: Run visualization tests | |
| timeout-minutes: 3 | |
| run: tox -e visualization | |
| - name: Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| external: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.10'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install julia | |
| uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: 1.7 | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-external | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh base R | |
| - name: Run tests | |
| timeout-minutes: 15 | |
| run: tox -e external | |
| - name: Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| petab: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-petab | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 20 | |
| run: tox -e petab | |
| - name: Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| mac: | |
| runs-on: macos-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11', '3.10'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/Library/Caches/pip | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-mac | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh | |
| - name: Run tests | |
| timeout-minutes: 10 | |
| run: tox -e mac | |
| - name: Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| notebooks1: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-notebooks1 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh | |
| - name: Run notebooks | |
| timeout-minutes: 15 | |
| run: tox -e notebooks1 | |
| notebooks2: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-notebooks2 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh R amici | |
| - name: Run notebooks | |
| timeout-minutes: 15 | |
| run: tox -e notebooks2 | |
| quality: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v1 | |
| with: | |
| path: ~/.cache | |
| key: ci-${{ runner.os }}-${{ matrix.python-version }}-quality | |
| - name: Install dependencies | |
| run: | | |
| .github/workflows/install_deps.sh doc | |
| pip install tox | |
| - name: Run quality checks | |
| timeout-minutes: 5 | |
| run: tox -e project,flake8 | |
| - name: Build docs | |
| timeout-minutes: 5 | |
| run: tox -e doc | |
| - name: Test migration | |
| timeout-minutes: 5 | |
| run: tox -e migrate | |
| - name: Coverage | |
| uses: codecov/codecov-action@v2 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml |