Relative: fix log of zero for default 0 sigma values #3982
Workflow file for this run
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| name: CI | |
| # trigger | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - develop | |
| pull_request: | |
| workflow_dispatch: | |
| schedule: | |
| # run Monday and Thursday at 03:42 UTC | |
| - cron: '42 3 * * MON,THU' | |
| env: | |
| # use all available cores for compiling amici models | |
| AMICI_PARALLEL_COMPILE: "" | |
| # non-interactive backend for matplotlib | |
| MPLBACKEND: "agg" | |
| # 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run tests | |
| timeout-minutes: 30 | |
| run: tox -e base | |
| env: | |
| CC: clang | |
| CXX: clang++ | |
| - 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/pip | |
| .tox/ | |
| 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: Cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~\AppData\Local\pip\Cache | |
| .tox | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci | |
| - 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici pysb | |
| - name: Run tests | |
| timeout-minutes: 35 | |
| run: tox -e petab | |
| env: | |
| CC: clang | |
| CXX: clang++ | |
| - 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'] | |
| # needed to allow julia-actions/cache to delete old caches that it has created | |
| permissions: | |
| actions: write | |
| contents: read | |
| 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 tox and cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.cache/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install julia | |
| uses: julia-actions/setup-julia@v1 | |
| with: | |
| version: 1.9 | |
| - name: Cache Julia | |
| uses: julia-actions/cache@v1 | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh | |
| - name: Install PEtabJL dependencies | |
| run: > | |
| julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0")); | |
| 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: | |
| # ipopt does not work on 3.9 (https://github.com/mechmotum/cyipopt/issues/225) | |
| 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh ipopt | |
| - name: Run tests | |
| timeout-minutes: 25 | |
| 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install dependencies | |
| run: pip install tox pre-commit | |
| - name: Check repository size | |
| run: tox -e size | |
| - 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - 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: 30 | |
| 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - 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/pip | |
| .tox/ | |
| key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }} | |
| - name: Install dependencies | |
| run: .github/workflows/install_deps.sh amici | |
| - name: Run notebooks 2 | |
| timeout-minutes: 20 | |
| run: tox -e notebooks2 |