Update Dependencies (#664) #1203
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| name: CI | |
| on: | |
| push: | |
| branches: [main, develop] | |
| pull_request: | |
| schedule: | |
| - cron: "18 15 * * MON" | |
| jobs: | |
| tests: | |
| name: ${{ matrix.toxenv }} (${{ matrix.python }} • ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Fast PR matrix | |
| - os: ubuntu-latest | |
| python: "3.13" | |
| toxenv: base | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| toxenv: base | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: base | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: visualization | |
| # macOS sanity | |
| - os: macos-latest | |
| python: "3.11" | |
| toxenv: mac | |
| # Quality | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: quality | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: project | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: doc | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: migrate | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: external-R | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: external-other-simulators | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: petab | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: base-notebooks | |
| - os: ubuntu-latest | |
| python: "3.11" | |
| toxenv: external-notebooks | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: pip | |
| - name: Install Julia | |
| if: ${{ startsWith(matrix.toxenv, 'external-') }} | |
| uses: julia-actions/setup-julia@v2 | |
| with: | |
| version: "1" # Use the latest stable Julia version | |
| - name: Install Julia dependencies | |
| if: ${{ startsWith(matrix.toxenv, 'external-') }} | |
| env: | |
| # make Julia/PyCall bind to the same Python used by the job | |
| PYTHON: ${{ env.pythonLocation }}/bin/python | |
| run: | | |
| julia -e 'using Pkg; Pkg.add("PyCall")' | |
| - name: Install R | |
| if: ${{ startsWith(matrix.toxenv, 'external-') }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - name: Install dependencies | |
| run: | | |
| case "${{ matrix.toxenv }}" in | |
| base|visualization|mac|base-notebooks) .github/workflows/install_deps.sh base ;; | |
| petab) .github/workflows/install_deps.sh amici ;; | |
| external-*) .github/workflows/install_deps.sh base amici ;; | |
| lint|project|doc|migrate) .github/workflows/install_deps.sh doc ;; | |
| esac | |
| python -m pip install -U pip tox | |
| - name: Run tox | |
| run: tox -e ${{ matrix.toxenv }} | |
| # If each tox env generates coverage.xml, include flags; otherwise combine explicitly | |
| - name: Upload coverage | |
| if: ${{ always() && matrix.os == 'ubuntu-latest' }} | |
| uses: codecov/codecov-action@v6 | |
| continue-on-error: true | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage.xml | |
| flags: ${{ matrix.toxenv }} |