Documentation fixes #2793
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: | |
| 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-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 | |
| mac: | |
| runs-on: macos-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 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 30 | |
| run: tox -e base | |
| - name: Coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| windows: | |
| runs-on: windows-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: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install tox | |
| - name: Run tests | |
| shell: bash | |
| timeout-minutes: 10 | |
| run: tox -e windows | |
| 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: 1.9 | |
| - 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: Install PEtabJL dependencies | |
| run: julia -e 'using Pkg; Pkg.add("PEtab"); Pkg.add("OrdinaryDiffEq"), Pkg.add("Sundials")' | |
| - name: Run tests | |
| timeout-minutes: 25 | |
| 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 |