trace equilibration times and total simulation time #2677
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| name: CI | |
| # trigger | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| schedule: | |
| # run Monday and Thursday at 03:42 UTC | |
| - cron: '42 3 * * MON,THU' | |
| # jobs | |
| jobs: | |
| base: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # update to 3.11 when numba allows (needed in umap) | |
| python-version: ['3.9', '3.10'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-base | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 25 | |
| run: tox -e base | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| petab: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-petab | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici pysb | |
| - name: Run tests | |
| timeout-minutes: 35 | |
| run: tox -e petab | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| julia: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - 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@v3 | |
| with: | |
| path: | | |
| ~/.cache | |
| ~/.julia/artifacts | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-julia | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh | |
| - name: Run tests | |
| timeout-minutes: 20 | |
| run: tox -e julia | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| optimize: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # update to 3.11 when nlopt allows | |
| python-version: ['3.9', '3.10'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-optimize | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh ipopt | |
| - name: Run tests | |
| timeout-minutes: 20 | |
| run: tox -e optimize | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| hierarchical: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-hierarchical | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 20 | |
| run: tox -e hierarchical | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| select: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-select | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 20 | |
| run: tox -e select | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| quality: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-quality | |
| - name: Install dependencies | |
| run: pip install tox pre-commit | |
| - name: Check repository size | |
| run: tox -e size | |
| - name: Run quality checks | |
| timeout-minutes: 5 | |
| run: tox -e project,flake8 | |
| - name: Run pre-commit hooks | |
| run: pre-commit run --all-files | |
| docs: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.11'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-docs | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh doc amici | |
| - name: Validate CITATION.cff | |
| run: pip install cffconvert && cffconvert --validate | |
| - name: Build doc | |
| timeout-minutes: 10 | |
| run: tox -e doc | |
| notebooks1: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks1 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici ipopt | |
| - name: Run notebooks 1 | |
| timeout-minutes: 20 | |
| run: tox -e notebooks1 | |
| notebooks2: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.9'] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Prepare python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks2 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run notebooks 2 | |
| timeout-minutes: 20 | |
| run: tox -e notebooks2 |