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Update example formatting for better sphinx-gallery rendering #5802

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Update example formatting for better sphinx-gallery rendering

Update example formatting for better sphinx-gallery rendering #5802

Workflow file for this run

.github/workflows/main.yml at 2e6d7ee
name: CI
on:
push:
# Build on tags that look like releases
tags:
- v*
# Build when main or testing is pushed to
branches:
- main
- testing
pull_request:
# Build when a pull request targets main
branches:
- main
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
matlab-test:
name: Run MATLAB Test Script
runs-on: ubuntu-latest
env:
LD_PRELOAD: /usr/lib/x86_64-linux-gnu/libstdc++.so.6
CANTERA_ROOT: /home/runner/work/cantera/cantera
CANTERA_DATA: /home/runner/work/cantera/cantera/data
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: '3.10'
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libopenmpi-dev libblas-dev \
liblapack-dev libhdf5-dev
gcc --version
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: |
python3 -m pip install ruamel.yaml scons==3.1.2
- name: Build Cantera
run: |
python3 `which scons` build env_vars=all -j4 debug=n --debug=time \
cc_flags=-D_GLIBCXX_ASSERTIONS
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v2
- name: Run tests
uses: matlab-actions/run-tests@v2
with:
select-by-folder: /home/runner/work/cantera/cantera/test/matlab_experimental
ubuntu-multiple-pythons:
name: ${{ matrix.os }} with Python ${{ matrix.python-version }}, Numpy ${{ matrix.numpy || 'latest' }}, Cython ${{ matrix.cython || 'latest' }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
strategy:
matrix:
python-version: ['3.8', '3.10', '3.11', '3.12', '3.13']
os: ['ubuntu-20.04', 'ubuntu-22.04']
numpy: ['']
cython: ['']
include:
# Keep some test cases with NumPy 1.x until we drop support
- python-version: '3.12'
os: 'ubuntu-24.04'
numpy: "'<2.0'"
# Keep some test cases with older Cython versions
- python-version: '3.10'
os: 'ubuntu-24.04'
cython: "==0.29.31" # minimum supported version
- python-version: '3.11'
os: 'ubuntu-24.04'
cython: "==3.0.8" # System version for Ubuntu 24.04
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libopenmpi-dev libblas-dev \
liblapack-dev libhdf5-dev libfmt-dev
gcc --version
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: |
python3 -m pip install ruamel.yaml scons==3.1.2 numpy${{ matrix.numpy }} \
cython${{ matrix.cython }} pandas pytest \
pytest-github-actions-annotate-failures pytest-xdist pint graphviz
- name: Build Cantera
run: |
python3 `which scons` build env_vars=all -j4 debug=n --debug=time \
system_fmt=y cc_flags=-D_GLIBCXX_ASSERTIONS
- name: Upload shared library
# Pin to 4.3.4 to resolve errors around only uploading symlinks.
# See https://github.com/actions/upload-artifact/issues/589
uses: actions/[email protected]
if: matrix.python-version == '3.11'
with:
path: build/lib/libcantera_shared.so
name: libcantera_shared-${{ matrix.os }}.so
retention-days: 2
- name: Build Tests
run:
python3 `which scons` -j4 build-tests --debug=time
- name: Run compiled tests
run: python3 `which scons` test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
LD_LIBRARY_PATH=build/lib
python3 -m pytest -raP -v -n auto --durations=50 test/python
- name: Save the wheel file to install Cantera
uses: actions/upload-artifact@v4
with:
path: build/python/dist/Cantera*.whl
retention-days: 2
name: cantera-wheel-${{ matrix.python-version }}-${{ matrix.os }}
if-no-files-found: error
clang-compiler:
name: LLVM/Clang with Python 3.8
runs-on: ubuntu-22.04
timeout-minutes: 60
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: 3.8
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libomp-dev libomp5 libopenblas-dev libhdf5-dev
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: python3 -m pip install ruamel.yaml scons numpy cython pandas pytest
pytest-xdist pytest-github-actions-annotate-failures pint graphviz
- name: Build Cantera
run: python3 `which scons` build env_vars=all
CXX=clang++-14 CC=clang-14 f90_interface=n extra_lib_dirs=/usr/lib/llvm/lib
-j4 debug=n --debug=time logging=debug
warning_flags='-Wall -Werror -Wsuggest-override'
- name: Build Tests
run:
python3 `which scons` -j4 build-tests --debug=time
- name: Run compiled tests
run: python3 `which scons` test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
LD_LIBRARY_PATH=build/lib
python3 -m pytest -raP -v -n auto --durations=50 test/python
macos-multiple-pythons:
name: ${{ matrix.macos-version }} with Python ${{ matrix.python-version }}
runs-on: ${{ matrix.macos-version }}
timeout-minutes: 90
strategy:
matrix:
macos-version: ['macos-13', 'macos-14', 'macos-15']
python-version: ['3.12', '3.13']
include:
- macos-version: 'macos-13'
python-version: '3.8'
- macos-version: 'macos-14'
python-version: '3.10'
extra-build-args: cxx_flags='-std=c++20'
- macos-version: 'macos-15'
python-version: '3.11'
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Write dependencies to a file for caching
run: |
echo "scons ruamel.yaml numpy cython pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz" | tr " " "\n" > requirements.txt
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: pip
cache-dependency-path: requirements.txt
- name: Install Brew dependencies
run: brew install --display-times boost libomp hdf5
- name: Set Include folder
run:
echo "BOOST_INC_DIR=$(brew --prefix)/include" >> $GITHUB_ENV
- name: Upgrade pip
run: python -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: python -m pip install -r requirements.txt
- name: Build Cantera
run: scons build env_vars=all -j3 debug=n --debug=time
boost_inc_dir=${BOOST_INC_DIR} ${{ matrix.extra-build-args }}
- name: Upload shared library
# Pin to 4.3.4 to resolve errors around only uploading symlinks.
# See https://github.com/actions/upload-artifact/issues/589
uses: actions/[email protected]
if: matrix.python-version == '3.12' && matrix.macos-version == 'macos-13'
with:
path: build/lib/libcantera_shared.dylib
name: libcantera_shared.dylib
retention-days: 2
- name: Build Tests
run: scons -j3 build-tests --debug=time
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
export DYLD_LIBRARY_PATH=build/lib
python3 -m pytest -raP -v -n auto --durations=50 test/python
# Coverage is its own job because macOS builds of the samples
# use Homebrew gfortran which is not compatible for coverage
# with XCode clang. Also, turning off optimization really
# slows down the tests
coverage:
name: Coverage
runs-on: ubuntu-latest
timeout-minutes: 90
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Setup python
uses: actions/setup-python@v5
with:
python-version: '3.11'
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran liblapack-dev libblas-dev libsundials-dev libhdf5-dev
gcc --version
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: |
python3 -m pip install ruamel.yaml scons numpy cython pandas scipy pytest \
pytest-github-actions-annotate-failures pytest-cov gcovr!=7.0.0 pint graphviz \
Jinja2
- name: Setup .NET Core SDK
uses: actions/setup-dotnet@v4
with:
dotnet-version: '6.x'
- name: Build Cantera
run: |
python3 `which scons` build blas_lapack_libs=lapack,blas coverage=y \
optimize=n skip_slow_tests=y no_optimize_flags='-DNDEBUG -O0' \
FORTRANFLAGS='-O0' env_vars=all -j4 --debug=time
- name: Build Tests
run: python3 `which scons` -j4 build-tests --debug=time
- name: Run compiled tests
run: python3 `which scons` test-gtest test-legacy --debug=time
- name: Run Python tests
run: python3 `which scons` test-python show_long_tests=yes verbose_tests=yes
- name: Build the .NET interface
run: dotnet build
working-directory: interfaces/dotnet
- name: Test the .NET interface
# Collect coverage info using Coverlet (identified by magic string below)
run: |
dotnet test --collect:"XPlat Code Coverage"
mv Cantera.Tests/TestResults/*/coverage.cobertura.xml .
dotnet new tool-manifest
dotnet tool install --local dotnet-reportgenerator-globaltool
dotnet reportgenerator -reports:"coverage.cobertura.xml" -targetdir:"coveragereport" -reporttypes:Html
working-directory: interfaces/dotnet
- name: Process coverage files
run: |
gcovr --root . --exclude-unreachable-branches --exclude-throw-branches \
--exclude-directories '\.sconf_temp' --exclude-directories 'build/ext$' \
--exclude '.*ext.*' --exclude '(.+/)?_cantera\.cpp$' --exclude '^test.*' \
--xml coverage.xml --html-details htmlcoverage.html --txt
- name: Archive C++ coverage results
uses: actions/upload-artifact@v4
with:
name: cxx-coverage-report
path: htmlcoverage*
retention-days: 5
- name: Archive Python coverage results
uses: actions/upload-artifact@v4
with:
name: python-coverage-report
path: build/python-coverage*
retention-days: 5
- name: Archive .NET coverage results
uses: actions/upload-artifact@v4
with:
name: dotnet-coverage-report
path: interfaces/dotnet/coveragereport*
retention-days: 5
- name: Upload Coverage to Codecov
uses: codecov/codecov-action@v5
with:
verbose: true
files: ./coverage.xml,./build/pycov.xml,./interfaces/dotnet/coverage.cobertura.xml
fail_ci_if_error: true
docs:
name: Build docs
runs-on: ubuntu-latest
timeout-minutes: 60
defaults:
run:
shell: bash -l {0}
env:
DEPLOY: ${{ github.event_name == 'push' && github.repository_owner == 'Cantera' && endsWith(github.ref, 'main') }}
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Set up micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-name: test-env
create-args: >-
python=3.11 doxygen=1.9.7 scons pip scikits.odes
post-cleanup: none
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev graphviz texlive-bibtex-extra \
libblas-dev liblapack-dev libhdf5-dev libfmt-dev libsundials-dev
- name: Upgrade pip
run: pip install -U pip setuptools wheel
- name: Install Python dependencies
# Pinned sphinx and pydata-sphinx-theme versions are for the Cantera 3.1.x
# series. These versions can be relaxed on main branch afterwards.
run: |
pip install ruamel.yaml scons numpy cython 'sphinx>=7.3.7,<7.4' sphinx-gallery \
sphinxcontrib-matlabdomain sphinxcontrib-doxylink sphinxcontrib-bibtex \
'pydata-sphinx-theme>=0.15.3,<0.16' sphinx-argparse sphinx_design myst-nb \
sphinx-copybutton matplotlib pandas scipy pint coolprop graphviz
pip install "git+https://github.com/Cantera/sphinx-tags.git@main"
- name: Build Cantera
run: scons build -j4 debug=n optimize=y use_pch=n
- name: Build documentation
run: |
scons sphinx doxygen logging=debug \
sphinx_options="-W --keep-going --warning-file=sphinx-warnings.txt"
- name: Show Sphinx warnings
run: |
cat sphinx-warnings.txt
if: failure()
- name: Ensure 'scons help' options work
run: |
scons help --options
scons help --list-options
scons help --option=prefix
- name: Create archive for docs output
run: |
cd build/doc
tar --exclude="*.map" --exclude="*.md5" -czf docs.tar.gz html
if: failure() || success()
- name: Store archive of docs output
uses: actions/upload-artifact@v4
with:
path: build/doc/docs.tar.gz
name: docs
retention-days: 14
if: failure() || success()
# The known_hosts key is generated with `ssh-keygen -F cantera.org` from a
# machine that has previously logged in to cantera.org and trusts
# that it logged in to the right machine
- name: Set up SSH key and host for deploy
if: env.DEPLOY == 'true'
uses: shimataro/ssh-key-action@v2
with:
key: ${{ secrets.CTDEPLOY_KEY }}
known_hosts: ${{ secrets.CTDEPLOY_HOST }}
- name: Upload the docs
if: env.DEPLOY == 'true'
env:
RSYNC_USER: "ctdeploy"
RSYNC_SERVER: "cantera.org"
RSYNC_DEST: "cantera/dev"
DOCS_OUTPUT_DIR: "./build/doc/html/"
run: |
rsync -avzP --checksum --exclude='*.map' --exclude='*.md5' \
--delete --delete-excluded --filter='P .htaccess' \
"${DOCS_OUTPUT_DIR}" ${RSYNC_USER}@${RSYNC_SERVER}:${RSYNC_DEST}
run-examples:
name: Run Python ${{ matrix.python-version }} examples on ${{ matrix.os }}, NumPy ${{ matrix.numpy || 'latest' }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
needs: ["ubuntu-multiple-pythons"]
strategy:
matrix:
# Keep some test cases with NumPy 1.x until we explicitly drop support
include:
- os: "ubuntu-20.04"
python-version: "3.8"
numpy: ""
- os: "ubuntu-22.04"
python-version: "3.8"
numpy: ""
- os: "ubuntu-20.04"
python-version: "3.10"
numpy: "==1.21.6"
- os: "ubuntu-22.04"
python-version: "3.10"
numpy: ""
- os: "ubuntu-22.04"
python-version: "3.11"
numpy: "==1.23.5"
- os: "ubuntu-20.04"
python-version: "3.11"
numpy: ""
- os: "ubuntu-22.04"
python-version: "3.12"
numpy: "==1.26.4"
- os: "ubuntu-20.04"
python-version: "3.12"
numpy: ""
- os: "ubuntu-22.04"
python-version: "3.13"
numpy: ""
fail-fast: false
steps:
# We're not building Cantera here, we only need the checkout for the samples
# folder, so no need to do a recursive checkout
- uses: actions/checkout@v4
name: Checkout the repository
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install graphviz libhdf5-103 libfmt-dev
- name: Download the wheel artifact
uses: actions/download-artifact@v4
with:
name: cantera-wheel-${{ matrix.python-version }}-${{ matrix.os }}
path: dist
- name: Download the Cantera shared library (.so)
uses: actions/download-artifact@v4
with:
name: libcantera_shared-${{ matrix.os }}.so
path: build/lib
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: |
python3 -m pip install numpy${{ matrix.numpy }} ruamel.yaml pandas pyarrow \
matplotlib scipy pint graphviz CoolProp
python3 -m pip install --pre --no-index --find-links dist cantera
- name: Run the examples
# See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part.
# Skip 1D_packed_bed.py due to difficulty installing scikits.odes.
# Increase figure limit to handle flame_speed_convergence_analysis.py.
# Skip equations_of_state.py in cases where CoolProp is broken (temporarily, for Python 3.13)
run: |
ln -s libcantera_shared.so build/lib/libcantera_shared.so.3
rm samples/python/reactors/1D_packed_bed.py
python3 -m CoolProp || rm samples/python/thermo/equations_of_state.py
echo "figure.max_open_warning: 100" > matplotlibrc
export LD_LIBRARY_PATH=build/lib
find samples/python -type f -iname "*.py" \
-exec sh -c 'for n; do echo "$n" | tee -a results.txt && python3 "$n" >> results.txt || exit 1; done' sh {} +
env:
# The pyparsing ignore setting is due to a new warning introduced in Matplotlib==3.6.0
# @todo: Remove the trapz-related ignore when dropping support for NumPy 1.x
# and replacing np.trapz with np.trapezoid
# Ignore NasaPoly2 warnings from n-hexane-NUIG-2015.yaml
PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing,ignore:datetime.datetime.utcfromtimestamp:DeprecationWarning:,ignore:`trapz`:DeprecationWarning,ignore:NasaPoly2:UserWarning:"
MPLBACKEND: Agg
- name: Save the results file for inspection
uses: actions/upload-artifact@v4
with:
path: results.txt
retention-days: 2
name: example-results-${{ matrix.python-version }}-${{ matrix.os }}-np${{ matrix.numpy || 'latest' }}
# Run this step if the job was successful or failed, but not if it was cancelled
# Using always() would run this step if the job was cancelled as well.
if: failure() || success()
multiple-sundials:
name: Sundials ${{ matrix.sundials-ver }} / fmt ${{ matrix.fmt-ver }}
runs-on: ubuntu-latest
timeout-minutes: 60
env:
PYTHON_VERSION: 3.8
defaults:
run:
shell: bash -l {0}
strategy:
matrix:
include:
- sundials-ver: 3
fmt-ver: 6.1.2
- sundials-ver: 4
fmt-ver: 8.1
- sundials-ver: 5.8
fmt-ver: 9.1
- sundials-ver: 6.4.1
fmt-ver: 10
- sundials-ver: 6.6
fmt-ver: 10
- sundials-ver: 7.0
fmt-ver: 11
extra-build-args: cxx_flags='-std=c++20'
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Set up micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-name: test-env
# See https://github.com/conda-forge/boost-cpp-feedstock/issues/41 for why we
# use boost-cpp rather than boost from conda-forge
create-args: >-
python=${{ env.PYTHON_VERSION }} sundials=${{ matrix.sundials-ver }} scons
numpy ruamel.yaml cython boost-cpp fmt=${{ matrix.fmt-ver }} eigen yaml-cpp
pandas libgomp openblas pytest pytest-xdist highfive python-graphviz
setuptools
post-cleanup: none
- name: Build Cantera
run: |
scons build system_fmt=y system_eigen=y system_yamlcpp=y system_sundials=y \
system_highfive=y blas_lapack_libs='lapack,blas' -j4 logging=debug debug=n \
optimize_flags='-O3 -ffast-math -fno-finite-math-only' \
${{ matrix.extra-build-args}}
- name: Test Cantera
run: scons test-zeroD test-python-reactor show_long_tests=yes verbose_tests=yes
- name: Test Install
# spot-check installation locations
run: |
scons install
test -f ${CONDA_PREFIX}/lib/libcantera_shared.so
test -f ${CONDA_PREFIX}/include/cantera/base/Solution.h
test -f ${CONDA_PREFIX}/bin/ck2yaml
test -f ${CONDA_PREFIX}/share/cantera/data/gri30.yaml
test -d ${CONDA_PREFIX}/share/cantera/samples
test -d ${CONDA_PREFIX}/share/cantera/samples/python
test -d ${CONDA_PREFIX}/lib/python${{ env.PYTHON_VERSION }}/site-packages/cantera
- name: Test Essentials
# ensure that Python package loads and converter scripts work
run: |
python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("3.1.0") else sys.exit(1)'
ck2yaml --input=test/data/h2o2.inp --output=h2o2-test.yaml
test -f h2o2-test.yaml
cti2yaml test/data/ch4_ion.cti ch4_ion-test.yaml
test -f ch4_ion-test.yaml
yaml2ck data/h2o2.yaml --mechanism=h2o2-test.ck
test -f h2o2-test.ck
windows-2022:
name: Windows 2022, Python ${{ matrix.python-version }}, fmt ${{ matrix.fmt-ver }}
runs-on: windows-2022
timeout-minutes: 60
strategy:
matrix:
include:
- python-version: '3.8'
fmt-ver: '10'
- python-version: '3.10'
fmt-ver: '8.1'
- python-version: '3.11'
fmt-ver: '9.1'
- python-version: '3.12'
fmt-ver: '7.1'
- python-version: '3.13'
fmt-ver: '11.0'
extra-build-args: cxx_flags='/EHsc /std:c++20 /utf-8'
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Set up micromamba
uses: mamba-org/setup-micromamba@v1
with:
environment-name: test-env
# See https://github.com/conda-forge/boost-cpp-feedstock/issues/41 for why we
# use boost-cpp rather than boost from conda-forge
# Install SCons >=4.4.0 to make sure that MSVC_TOOLSET_VERSION variable is present
create-args: >-
python=${{ matrix.python-version }} scons numpy cython ruamel.yaml boost-cpp
eigen yaml-cpp pandas pytest pytest-xdist highfive pint python-graphviz
fmt=${{ matrix.fmt-ver }} setuptools
post-cleanup: none
init-shell: powershell
- name: Build Cantera
run: scons build system_eigen=y system_yamlcpp=y system_highfive=y logging=debug
toolchain=msvc f90_interface=n debug=n ${{ matrix.extra-build-args }}
--debug=time -j4
- name: Upload shared library
# Pin to 4.3.4 to resolve errors around only uploading symlinks.
# See https://github.com/actions/upload-artifact/issues/589
uses: actions/[email protected]
if: matrix.python-version == '3.11'
with:
path: build/lib/cantera_shared.dll
name: cantera_shared.dll
retention-days: 2
- name: Build Tests
run: scons -j4 build-tests --debug=time
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
pytest -raP -v -n auto --durations=50 test/python
- name: Test Install
# spot-check installation locations
run: |
scons install
$paths = @('Library/bin/cantera_shared.dll',
'Library/include/cantera/base/Solution.h', 'Scripts/ck2yaml.exe',
'share/cantera/data/gri30.yaml', 'share/cantera/samples',
'share/cantera/samples/python', 'Lib/site-packages/cantera')
Foreach ($path in $paths) {
if (-not (Test-Path $Env:CONDA_PREFIX/$path)) {
echo "$path not found in install directory"
exit 1
}
}
- name: Test Essentials
# ensure that Python package loads and converter scripts work
run: |
python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("3.1.0") else sys.exit(1)'
ck2yaml --input=test/data/h2o2.inp --output=h2o2-test.yaml
if (-not (Test-Path h2o2-test.yaml)) { exit 1 }
cti2yaml test/data/ch4_ion.cti ch4_ion-test.yaml
if (-not (Test-Path ch4_ion-test.yaml)) { exit 1 }
yaml2ck data/h2o2.yaml --mechanism=h2o2-test.ck
if (-not (Test-Path h2o2-test.ck)) { exit 1 }
windows:
name: "Windows 2019, MSVC ${{ matrix.vs-toolset }}, Python ${{ matrix.python-version }}"
runs-on: windows-2019
timeout-minutes: 60
env:
BOOST_ROOT: ${{github.workspace}}/3rdparty/boost
BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z
strategy:
matrix:
vs-toolset: ['14.2']
python-version: ["3.8", "3.10", "3.11", "3.12", "3.13"]
fail-fast: false
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Set Up Python
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install Python dependencies
run: |
python -m pip install -U pip setuptools wheel
python -m pip install 'scons<4.4.0' pypiwin32 numpy ruamel.yaml cython pandas graphviz pytest pytest-xdist pytest-github-actions-annotate-failures
- name: Restore Boost cache
uses: actions/cache@v4
id: cache-boost
with:
path: ${{env.BOOST_ROOT}}
key: boost-178-win
- name: Install Boost Headers
if: steps.cache-boost.outputs.cache-hit != 'true'
run: |
BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g')
mkdir -p $BOOST_ROOT
curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL
7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost
mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost
rm $BOOST_ROOT/download.7z
shell: bash
- name: Build Cantera
run: scons build -j4 boost_inc_dir=$Env:BOOST_ROOT debug=n logging=debug
python_package=y env_vars=USERPROFILE,GITHUB_ACTIONS
msvc_version=${{ matrix.vs-toolset }} f90_interface=n --debug=time
- name: Build Tests
run: scons -j4 build-tests --debug=time
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: python -m pytest -raP -v -n auto --durations=50 test/python
# Adapted from https://www.scivision.dev/intel-oneapi-github-actions/
linux-intel-oneapi:
name: intel-oneAPI on Ubuntu, Python 3.8
runs-on: ubuntu-latest
timeout-minutes: 60
env:
INTEL_REPO: https://apt.repos.intel.com
INTEL_KEY: GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
steps:
- name: Intel Apt repository
timeout-minutes: 1
run: |
wget ${INTEL_REPO}/intel-gpg-keys/${INTEL_KEY}
sudo apt-key add ${INTEL_KEY}
rm ${INTEL_KEY}
echo "deb ${INTEL_REPO}/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
sudo apt-get update
- name: Install Intel oneAPI
timeout-minutes: 15
run: |
sudo apt-get install intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic \
intel-oneapi-mpi intel-oneapi-mpi-devel intel-oneapi-mkl ninja-build libboost-dev libhdf5-dev
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: 3.8
architecture: x64
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
run: |
python3 -m pip install ruamel.yaml scons numpy cython pandas pytest \
pytest-xdist pytest-github-actions-annotate-failures pint graphviz
- name: Setup Intel oneAPI environment
run: |
source /opt/intel/oneapi/setvars.sh
printenv >> $GITHUB_ENV
- name: Build Cantera
run: python3 `which scons` build env_vars=all CC=icx CXX=icpx -j4 debug=n
--debug=time f90_interface=n # FORTRAN=ifx
- name: Build Tests
run: python3 `which scons` -j4 build-tests --debug=time
- name: Run compiled tests
run: python3 `which scons` test-gtest test-legacy --debug=time
- name: Run Python tests
run: |
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:build/lib
python3 -m pytest -raP -v -n auto --durations=50 test/python
windows-mingw:
name: mingw on Windows, Python 3.10
runs-on: windows-2022
timeout-minutes: 120 # MinGW is slooooow
env:
BOOST_ROOT: ${{github.workspace}}/3rdparty/boost
BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z
steps:
- uses: actions/checkout@v4
name: Checkout the repository
with:
submodules: recursive
- name: Set Up Python
uses: actions/setup-python@v5
with:
python-version: "3.10"
architecture: x64
- name: Install Python dependencies
run: |
python -m pip install -U pip setuptools wheel
python -m pip install scons pypiwin32 numpy ruamel.yaml cython h5py pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz
- name: Restore Boost cache
uses: actions/cache@v4
id: cache-boost
with:
path: ${{env.BOOST_ROOT}}
key: boost-178-win
- name: Set up MinGW
uses: egor-tensin/setup-mingw@v2
with:
platform: x64
static: false
version: 12.2
- name: Install Boost Headers
if: steps.cache-boost.outputs.cache-hit != 'true'
run: |
BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g')
mkdir -p $BOOST_ROOT
curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL
7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost
mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost
rm $BOOST_ROOT/download.7z
shell: bash
- name: Build Cantera
run: scons build -j4 boost_inc_dir=$Env:BOOST_ROOT debug=n logging=debug
python_package=y env_vars=USERPROFILE,PYTHONPATH,GITHUB_ACTIONS
toolchain=mingw f90_interface=n --debug=time
- name: Upload Wheel
uses: actions/upload-artifact@v4
with:
path: build\python\dist\Cantera*.whl
name: Cantera-win_amd64.whl
retention-days: 2
- name: Build Tests
run: scons -j4 build-tests --debug=time
- name: Run compiled tests
run: scons test-gtest test-legacy --debug=time
- name: Run Python tests
run: python -m pytest -raP -v -n auto --durations=50 test/python
- name: Upload Test binaries
if: always()
uses: actions/upload-artifact@v4
with:
path: |
build/test/**/*.exe
build/lib/*.dll
name: mingw-gtest-binaries
retention-days: 2
dotnet:
name: .NET on ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-22.04, windows-2022, macos-13]
fail-fast: false
runs-on: ${{ matrix.os }}
needs: [ubuntu-multiple-pythons, macos-multiple-pythons, windows-2022]
timeout-minutes: 60
steps:
- uses: actions/checkout@v4
name: Checkout the repository
- name: Install Python dependencies
# Install for the default system Python 3, which is used by 'dotnet build'
run: python3 -m pip install ruamel.yaml Jinja2
- name: Install library dependencies with micromamba (Windows)
uses: mamba-org/setup-micromamba@v1
with:
environment-name: test-env
# fmt needs to match the version of the windows-2022 runner selected to upload
# the cantera_shared.dll artifact
create-args: >-
yaml-cpp mkl highfive fmt=9.1
init-shell: bash powershell
post-cleanup: none
if: matrix.os == 'windows-2022'
- name: Install Brew dependencies (macOS)
run: brew install --display-times hdf5
if: matrix.os == 'macos-13'
- name: Install Apt dependencies (Ubuntu)
run: |
sudo apt update
sudo apt install libhdf5-dev libfmt-dev
if: matrix.os == 'ubuntu-22.04'
- name: Setup .NET Core SDK
uses: actions/setup-dotnet@v4
with:
dotnet-version: '6.x'
- name: Download the Cantera shared library (.so)
uses: actions/download-artifact@v4
with:
name: libcantera_shared-ubuntu-22.04.so
path: build/lib
- name: Download the Cantera shared library (.dylib)
uses: actions/download-artifact@v4
with:
name: libcantera_shared.dylib
path: build/lib
- name: Download the Cantera shared library (.dll)
uses: actions/download-artifact@v4
with:
name: cantera_shared.dll
path: build/lib
- name: Build the .NET interface
run: dotnet build
working-directory: interfaces/dotnet
- name: Test the .NET interface
run: dotnet test
working-directory: interfaces/dotnet
- name: Run the .NET samples
run: |
dotnet run --project examples/Application
dotnet run --project examples/SoundSpeed
working-directory: interfaces/dotnet