Updated readthedocs.yml to linkcheck #11321
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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
- name: Setup Python | |
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
- name: Install Linux system dependencies | |
uses: awalsh128/cache-apt-pkgs-action@a6c3917cc929dd0345bfb2d3feaf9101823370ad # v1.4.2 | |
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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
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@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0 | |
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/codecov-action@1e68e06f1dbfde0e4cefc87efeba9e4643565303 # v5.1.2 | |
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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
with: | |
fetch-depth: 0 | |
- name: Install Linux system dependencies | |
uses: awalsh128/cache-apt-pkgs-action@a6c3917cc929dd0345bfb2d3feaf9101823370ad # v1.4.2 | |
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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
- name: Install Linux system dependencies | |
uses: awalsh128/cache-apt-pkgs-action@a6c3917cc929dd0345bfb2d3feaf9101823370ad # v1.4.2 | |
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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
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@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0 | |
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@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
- name: Install Linux system dependencies | |
uses: awalsh128/cache-apt-pkgs-action@a6c3917cc929dd0345bfb2d3feaf9101823370ad # v1.4.2 | |
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@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0 | |
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@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0 | |
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 |