Fix BPX bug when activation energies not provided #11125
Workflow file for this run
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| name: PyBaMM | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| env: | |
| PYBAMM_DISABLE_TELEMETRY: "true" | |
| FORCE_COLOR: 3 | |
| PYBAMM_IDAKLU_EXPR_CASADI: ON | |
| PYBAMM_IDAKLU_EXPR_IREE: ON | |
| concurrency: | |
| # github.workflow: name of the workflow, so that we don't cancel other workflows | |
| # github.event.pull_request.number || github.ref: pull request number or branch name if not a pull request | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| # Cancel in-progress runs when a new workflow with the same group name is triggered | |
| # This avoids workflow runs on both pushes and PRs | |
| cancel-in-progress: true | |
| jobs: | |
| style: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Set up uv | |
| run: python -m pip install uv | |
| - name: Check style | |
| run: | | |
| python -m uv pip install pre-commit | |
| pre-commit run -a | |
| run_unit_integration_and_coverage_tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-13, macos-14, windows-latest] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| name: Tests (${{ matrix.os }} / Python ${{ matrix.python-version }}) | |
| steps: | |
| - name: Check out PyBaMM repository | |
| uses: actions/checkout@v4 | |
| - name: Install Linux system dependencies | |
| uses: awalsh128/[email protected] | |
| if: matrix.os == 'ubuntu-latest' | |
| with: | |
| packages: gfortran gcc graphviz pandoc | |
| execute_install_scripts: true | |
| # dot -c is for registering graphviz fonts and plugins | |
| - name: Install OpenBLAS and TeXLive for Linux | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| sudo apt-get update | |
| sudo dot -c | |
| sudo apt-get install libopenblas-dev texlive-latex-extra dvipng | |
| - name: Install macOS system dependencies | |
| if: matrix.os == 'macos-13' || matrix.os == 'macos-14' | |
| env: | |
| HOMEBREW_NO_INSTALL_CLEANUP: 1 | |
| HOMEBREW_NO_AUTO_UPDATE: 1 | |
| HOMEBREW_NO_COLOR: 1 | |
| # Speed up CI | |
| NONINTERACTIVE: 1 | |
| # sometimes gfortran cannot be found, so reinstall gcc just to be sure | |
| run: | | |
| brew analytics off | |
| brew install graphviz libomp | |
| brew reinstall gcc | |
| - name: Install Windows system dependencies | |
| if: matrix.os == 'windows-latest' | |
| run: choco install graphviz --version=8.0.5 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Set up uv | |
| run: python -m pip install uv | |
| - name: Install nox | |
| run: python -m uv pip install nox[uv] | |
| - name: Cache pybamm-requires nox environment for GNU/Linux and macOS | |
| uses: actions/cache@v4 | |
| if: matrix.os != 'windows-latest' | |
| with: | |
| path: | | |
| # Repository files | |
| ${{ github.workspace }}/pybind11/ | |
| ${{ github.workspace }}/install_KLU_Sundials/ | |
| # Headers and dynamic library files for SuiteSparse and SUNDIALS | |
| ${{ env.HOME }}/.local/lib/ | |
| ${{ env.HOME }}/.local/include/ | |
| key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }} | |
| - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS | |
| timeout-minutes: 10 | |
| if: matrix.os != 'windows-latest' | |
| run: python -m nox -s pybamm-requires | |
| - name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| if: matrix.os != 'ubuntu-latest' || matrix.python-version != '3.12' | |
| run: python -m nox -s unit | |
| - name: Run coverage tests for ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| run: python -m nox -s coverage | |
| - name: Upload coverage report | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| uses: codecov/[email protected] | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }} | |
| run: python -m nox -s integration | |
| # Skips IDAKLU module compilation for speedups, which is already tested in other jobs. | |
| run_doctests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| name: Doctests (ubuntu-latest / Python 3.11) | |
| steps: | |
| - name: Check out PyBaMM repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install Linux system dependencies | |
| uses: awalsh128/[email protected] | |
| with: | |
| packages: graphviz pandoc | |
| execute_install_scripts: true | |
| # dot -c is for registering graphviz fonts and plugins | |
| - name: Install TeXLive for Linux | |
| run: | | |
| sudo apt-get update | |
| sudo dot -c | |
| sudo apt-get install texlive-latex-extra dvipng | |
| - name: Set up Python | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| cache: 'pip' | |
| - name: Set up uv | |
| run: python -m pip install uv | |
| - name: Install nox | |
| run: python -m uv pip install nox[uv] | |
| - name: Install docs dependencies and run doctests for GNU/Linux | |
| run: python -m nox -s doctests | |
| - name: Check if the documentation can be built for GNU/Linux | |
| run: python -m nox -s docs | |
| run_example_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| name: Example notebooks (ubuntu-latest / Python 3.12) | |
| steps: | |
| - name: Check out PyBaMM repository | |
| uses: actions/checkout@v4 | |
| - name: Install Linux system dependencies | |
| uses: awalsh128/[email protected] | |
| with: | |
| packages: gfortran gcc graphviz pandoc | |
| execute_install_scripts: true | |
| # dot -c is for registering graphviz fonts and plugins | |
| - name: Install OpenBLAS and TeXLive for Linux | |
| run: | | |
| sudo apt-get update | |
| sudo dot -c | |
| sudo apt-get install libopenblas-dev texlive-latex-extra dvipng | |
| - name: Set up Python 3.12 | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| cache: 'pip' | |
| - name: Set up uv | |
| run: python -m pip install uv | |
| - name: Install nox | |
| run: python -m uv pip install nox[uv] | |
| - name: Cache pybamm-requires nox environment for GNU/Linux | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| # Repository files | |
| ${{ github.workspace }}/pybind11/ | |
| ${{ github.workspace }}/install_KLU_Sundials/ | |
| # Headers and dynamic library files for SuiteSparse and SUNDIALS | |
| ${{ env.HOME }}/.local/lib/ | |
| ${{ env.HOME }}/.local/include/ | |
| key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }} | |
| - name: Install SuiteSparse and SUNDIALS on GNU/Linux | |
| timeout-minutes: 10 | |
| run: python -m nox -s pybamm-requires | |
| - name: Run example notebooks tests for GNU/Linux with Python 3.12 | |
| run: python -m nox -s examples | |
| run_scripts_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| name: Example scripts (ubuntu-latest / Python 3.12) | |
| steps: | |
| - name: Check out PyBaMM repository | |
| uses: actions/checkout@v4 | |
| - name: Install Linux system dependencies | |
| uses: awalsh128/[email protected] | |
| with: | |
| packages: gfortran gcc graphviz | |
| execute_install_scripts: true | |
| # dot -c is for registering graphviz fonts and plugins | |
| - name: Install OpenBLAS and TeXLive for Linux | |
| run: | | |
| sudo apt-get update | |
| sudo dot -c | |
| sudo apt-get install libopenblas-dev texlive-latex-extra dvipng | |
| - name: Set up Python 3.12 | |
| id: setup-python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| cache: 'pip' | |
| - name: Set up uv | |
| run: python -m pip install uv | |
| - name: Install nox | |
| run: python -m uv pip install nox[uv] | |
| - name: Cache pybamm-requires nox environment for GNU/Linux | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| # Repository files | |
| ${{ github.workspace }}/pybind11/ | |
| ${{ github.workspace }}/install_KLU_Sundials/ | |
| # Headers and dynamic library files for SuiteSparse and SUNDIALS | |
| ${{ env.HOME }}/.local/lib/ | |
| ${{ env.HOME }}/.local/include/ | |
| key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }} | |
| - name: Install SuiteSparse and SUNDIALS on GNU/Linux | |
| timeout-minutes: 10 | |
| run: python -m nox -s pybamm-requires | |
| - name: Run example scripts tests for GNU/Linux with Python 3.12 | |
| run: python -m nox -s scripts |