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Doxygen cleanup

Doxygen cleanup #4356

Workflow file for this run

.github/workflows/main.yml at 7fdd044
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@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: '3.10'
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libopenmpi-dev libpython3-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 -j2 debug=n --debug=time \
cc_flags=-D_GLIBCXX_ASSERTIONS
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v1
- name: Run tests
uses: matlab-actions/run-tests@v1
with:
select-by-folder: /home/runner/work/cantera/cantera/test/matlab_experimental
ubuntu-multiple-pythons:
name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
strategy:
matrix:
python-version: ['3.8', '3.10', '3.11']
os: ['ubuntu-20.04', 'ubuntu-22.04']
fail-fast: false
env:
HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCLUDEDIR: /usr/include/hdf5/serial
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev gfortran libopenmpi-dev libpython3-dev \
libblas-dev liblapack-dev libhdf5-dev libfmt-dev
gcc --version
- name: Upgrade pip
run: python3 -m pip install -U pip setuptools wheel
- name: Install Python dependencies
# h5py is optional; some versions don't have binaries (yet)
run: |
python3 -m pip install ruamel.yaml scons==3.1.2 numpy cython pandas pytest \
pytest-github-actions-annotate-failures pint
python3 -m pip install h5py
- name: Build Cantera
run: |
python3 `which scons` build env_vars=all -j2 debug=n --debug=time \
system_fmt=y hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR \
cc_flags=-D_GLIBCXX_ASSERTIONS
- name: Upload shared library
uses: actions/upload-artifact@v3
if: matrix.python-version == '3.10'
with:
path: build/lib/libcantera_shared.so
name: libcantera_shared-${{ matrix.os }}.so
retention-days: 2
- name: Test Cantera
run:
python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
- name: Save the wheel file to install Cantera
uses: actions/upload-artifact@v3
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
env:
HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCLUDEDIR: /usr/include/hdf5/serial
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
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 h5py pytest pytest-github-actions-annotate-failures pint
- name: Build Cantera
run: python3 `which scons` build env_vars=all
CXX=clang++-12 CC=clang-12 f90_interface=n extra_lib_dirs=/usr/lib/llvm/lib
-j2 debug=n --debug=time hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR
- name: Test Cantera
run:
python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
macos-multiple-pythons:
name: macOS with Python ${{ matrix.python-version }}
runs-on: macos-11
timeout-minutes: 90
strategy:
matrix:
python-version: ['3.8', '3.10', '3.11']
fail-fast: false
env:
PYTHON_CMD: "python${{ matrix.python-version }}"
steps:
# Attempt to fix intermittent cloning errors. The error message says something like
# error: RPC failed; curl 18 transfer closed with outstanding read data remaining
# The clone is already being done with --depth=1, so the next recommended fix is to
# increase the buffer size. See also:
# https://github.com/actions/virtual-environments/issues/2198
# https://stackoverflow.com/q/38618885
- name: Configure git
run: /usr/local/bin/git config --global http.postBuffer 1048576000
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup GH Python
uses: actions/setup-python@v4
with:
python-version: 3.11
if: matrix.python-version == '3.11'
- name: Install Brew dependencies
run: brew install --display-times boost libomp hdf5
- name: Setup Homebrew Python
# This path should work for future Python versions as well
if: matrix.python-version != '3.11'
run: |
brew install --display-times python@${{ matrix.python-version }}
brew link --force --overwrite python@${{ matrix.python-version }}
brew install --display-times scons
- name: Upgrade pip
run: $PYTHON_CMD -m pip install -U pip 'setuptools>=47.0.0,<48' wheel
- name: Install Python dependencies
# h5py is optional; may fail if no wheel is present for a given OS/Python version
run: |
$PYTHON_CMD -m pip install ruamel.yaml numpy cython pandas pytest pytest-github-actions-annotate-failures pint
$PYTHON_CMD -m pip install h5py || true
- name: Install Python dependencies for GH Python
if: matrix.python-version == '3.11'
run:
$PYTHON_CMD -m pip install scons
- name: Build Cantera
run: scons build env_vars=all -j3 python_cmd=$PYTHON_CMD debug=n --debug=time
- name: Upload shared library
uses: actions/upload-artifact@v3
if: matrix.python-version == '3.10'
with:
path: build/lib/libcantera_shared.dylib
name: libcantera_shared.dylib
retention-days: 2
- name: Test Cantera
run:
scons test show_long_tests=yes verbose_tests=yes --debug=time
# 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
env:
HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCLUDEDIR: /usr/include/hdf5/serial
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup python
uses: actions/setup-python@v4
with:
python-version: '3.8'
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 h5py \
pytest-github-actions-annotate-failures pytest-cov gcovr pint
- name: Setup .NET Core SDK
uses: actions/setup-dotnet@v2
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 -j2 --debug=time \
hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR
- name: Test Cantera
run:
python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
- 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@v3
with:
name: cxx-coverage-report
path: htmlcoverage*
retention-days: 5
- name: Archive Python coverage results
uses: actions/upload-artifact@v3
with:
name: python-coverage-report
path: build/python-coverage*
retention-days: 5
- name: Archive .NET coverage results
uses: actions/upload-artifact@v3
with:
name: dotnet-coverage-report
path: interfaces/dotnet/coveragereport*
retention-days: 5
- name: Upload Coverage to Codecov
uses: codecov/codecov-action@v3
with:
verbose: true
files: ./coverage.xml,./build/pycov.xml,./interfaces/dotnet/coverage.cobertura.xml
fail_ci_if_error: true
example-keywords:
name: Check example keywords
runs-on: ubuntu-latest
timeout-minutes: 10
steps:
- uses: actions/checkout@v3
name: Checkout the repository
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: '3.10'
- name: Check keywords
run: python3 doc/example-keywords.py compare
docs:
name: Build docs
runs-on: ubuntu-latest
timeout-minutes: 60
env:
DEPLOY: ${{ github.event_name == 'push' && github.repository_owner == 'Cantera' && endsWith(github.ref, 'main') }}
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: '3.8'
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install libboost-dev doxygen graphviz texlive-bibtex-extra
- 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 sphinx\<4.0 jinja2\<3.1.0 \
sphinxcontrib-katex sphinxcontrib-matlabdomain sphinxcontrib-doxylink pint
- name: Build Cantera with documentation
run: python3 `which scons` build -j2 doxygen_docs=y sphinx_docs=y debug=n optimize=n use_pch=n
- name: Ensure 'scons help' options work
run: |
python3 `which scons` help --options
python3 `which scons` help --list-options
python3 `which scons` help --option=prefix
- name: Parse configuration options from SConstruct as reST
run: |
python3 `which scons` help --restructured-text --dev --output=config-options-dev.rst
mkdir build/docs/scons
mv config-options-dev.rst build/docs/scons/
- name: Create archive for docs output
run: |
cd build
tar -czf docs.tar.gz docs
- name: Store archive of docs output
uses: actions/upload-artifact@v3
with:
path: build/docs.tar.gz
name: docs
retention-days: 2
# 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: ${{ secrets.CTDEPLOY_HOST }}
- name: Upload the docs
if: env.DEPLOY == 'true'
env:
RSYNC_USER: "ctdeploy"
RSYNC_SERVER: "cantera.org"
RSYNC_DEST: "cantera/documentation/dev"
DOCS_OUTPUT_DIR: "./build/docs/"
run: |
rsync -avzP --checksum --exclude='*.map' --exclude='*.md5' \
--exclude='/doxygen/xml' --delete --delete-excluded \
"${DOCS_OUTPUT_DIR}" ${RSYNC_USER}@${RSYNC_SERVER}:${RSYNC_DEST}
run-examples:
name: Run Python ${{ matrix.python-version }} examples on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
needs: ["ubuntu-multiple-pythons"]
strategy:
matrix:
os: ["ubuntu-20.04", "ubuntu-22.04"]
python-version: ['3.8', '3.10', '3.11']
fail-fast: false
env:
HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCLUDEDIR: /usr/include/hdf5/serial
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@v3
name: Checkout the repository
- name: Setup Python
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install Apt dependencies
run: |
sudo apt update
sudo apt install graphviz libhdf5-103
- name: Download the wheel artifact
uses: actions/download-artifact@v3
with:
name: cantera-wheel-${{ matrix.python-version }}-${{ matrix.os }}
path: dist
- name: Download the Cantera shared library (.so)
uses: actions/download-artifact@v3
with:
name: libcantera_shared-${{ 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 ruamel.yaml h5py pandas matplotlib scipy pint
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
run: |
ln -s libcantera_shared.so build/lib/libcantera_shared.so.3
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 ignore setting here is due to a new warning introduced in Matplotlib==3.6.0
PYTHONWARNINGS: "error,ignore:warn_name_set_on_empty_Forward::pyparsing"
MPLBACKEND: Agg
- name: Save the results file for inspection
uses: actions/upload-artifact@v3
with:
path: results.txt
retention-days: 2
name: example-results
# 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: 7.1
- 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
fail-fast: false
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: ${{ env.PYTHON_VERSION }}
miniforge-version: latest
activate-environment: test
name: Set up conda
- name: Install conda dependencies
# See https://github.com/conda-forge/boost-cpp-feedstock/issues/41 for why we
# use boost-cpp rather than boost from conda-forge
run: |
conda install -q sundials=${{ matrix.sundials-ver }} scons numpy ruamel.yaml \
cython boost-cpp fmt=${{ matrix.fmt-ver }} eigen yaml-cpp h5py pandas \
libgomp openblas pytest highfive pint
- 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' -j2 logging=debug debug=n \
optimize_flags='-O3 -ffast-math -fno-finite-math-only'
- 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("3.0.0") 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: ${{ matrix.os }}, MSVC ${{ matrix.vs-toolset }}, Python ${{ matrix.python-version }}, fmt ${{ matrix.fmt-ver }}
runs-on: ${{ matrix.os }}
timeout-minutes: 60
defaults:
run:
shell: bash -l {0}
strategy:
matrix:
os: ["windows-2022"]
vs-toolset: ["14.1", "14.3"]
python-version: ["3.8", "3.10", "3.11"]
include:
- python-version: 3.8
fmt-ver: 10
- python-version: 3.10
fmt-ver: 8.1
- python-version: 3.11
fmt-ver: 7.1
fail-fast: false
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Set up conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: ${{ matrix.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: test
run-post: false
- name: Install conda dependencies
# See https://github.com/conda-forge/boost-cpp-feedstock/issues/41 for why we
# use boost-cpp rather than boost from conda-forge
# Install SCons >=4.4.0 to make sure that MSVC_TOOLSET_VERSION variable is present
run: |
mamba install -q '"scons>=4.4.0"' numpy cython ruamel.yaml boost-cpp eigen yaml-cpp h5py pandas pytest highfive pint fmt=${{ matrix.fmt-ver }}
shell: pwsh
- name: Build Cantera
run: scons build system_eigen=y system_yamlcpp=y system_highfive=y logging=debug
msvc_toolset_version=${{ matrix.vs-toolset }} f90_interface=n debug=n --debug=time -j2
shell: pwsh
- name: Upload shared library
uses: actions/upload-artifact@v3
if: matrix.python-version == '3.10' && matrix.vs-toolset == '14.3'
with:
path: build/lib/cantera_shared.dll
name: cantera_shared.dll
retention-days: 2
- name: Test Cantera
run: scons test show_long_tests=yes verbose_tests=yes --debug=time
shell: pwsh
- name: Test Install
# spot-check installation locations
run: |
set -x
scons install
test -f ${CONDA_PREFIX}/Library/bin/cantera_shared.dll
test -f ${CONDA_PREFIX}/Library/include/cantera/base/Solution.h
test -f ${CONDA_PREFIX}/Scripts/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/site-packages/cantera
- name: Test Essentials
# ensure that Python package loads and converter scripts work
run: |
set -x
python -c 'import cantera as ct; import sys; sys.exit(0) if ct.__version__.startswith("3.0.0") 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:
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"]
fail-fast: false
steps:
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Set Up Python
uses: actions/setup-python@v4
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 pytest pytest-github-actions-annotate-failures pint
- name: Restore Boost cache
uses: actions/cache@v3
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 $BOOST_ROOT/download.7z
shell: bash
- name: Build Cantera
run: scons build -j2 boost_inc_dir=%BOOST_ROOT% debug=n logging=debug
python_package=full env_vars=USERPROFILE,GITHUB_ACTIONS
msvc_version=${{ matrix.vs-toolset }} f90_interface=n --debug=time
shell: cmd
- name: Test Cantera
run: scons test show_long_tests=yes verbose_tests=yes --debug=time
# 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
HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial
HDF5_INCLUDEDIR: /usr/include/hdf5/serial
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@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
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 h5py pytest \
pytest-github-actions-annotate-failures pint
- name: Setup Intel oneAPI environment
run: |
source /opt/intel/oneapi/setvars.sh
printenv >> $GITHUB_ENV
- name: Build Cantera
run: python3 `which scons` build env_vars=all CC=icx CXX=icpx -j2 debug=n
hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR
--debug=time f90_interface=n # FORTRAN=ifx
- name: Test Cantera
run: |
python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
linux-intel-oneapi-classic:
name: intel-oneAPI classic 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
- uses: actions/checkout@v3
name: Checkout the repository
with:
submodules: recursive
- name: Setup Python
uses: actions/setup-python@v4
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 h5py pandas pytest
pytest-github-actions-annotate-failures pint
- 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=icc CXX=icpc -j2 debug=n
--debug=time f90_interface=n # FORTRAN=ifort
- name: Test Cantera
run:
python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time
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@v3
name: Checkout the repository
with:
submodules: recursive
- name: Set Up Python
uses: actions/setup-python@v4
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-github-actions-annotate-failures pint
- name: Restore Boost cache
uses: actions/cache@v3
id: cache-boost
with:
path: ${{env.BOOST_ROOT}}
key: boost-178-win
- name: Set up MinGW
uses: egor-tensin/setup-mingw@v2
with:
platform: x64
static: false
- name: Install Boost Headers
if: steps.cache-boost.outputs.cache-hit != 'true'
run: |
BOOST_ROOT=$(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 -j2 boost_inc_dir=%BOOST_ROOT% debug=n logging=debug
python_package=full env_vars=USERPROFILE,PYTHONPATH,GITHUB_ACTIONS
toolchain=mingw f90_interface=n --debug=time
shell: cmd
- name: Upload Wheel
uses: actions/upload-artifact@v3
with:
path: build\python\dist\Cantera*.whl
name: Cantera-win_amd64.whl
retention-days: 2
- name: Test Cantera
run: scons test show_long_tests=yes verbose_tests=yes --debug=time
- name: Upload Test binaries
if: always()
uses: actions/upload-artifact@v3
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-11]
fail-fast: false
runs-on: ${{ matrix.os }}
needs: [ubuntu-multiple-pythons, macos-multiple-pythons, windows-2022]
timeout-minutes: 60
steps:
- uses: actions/checkout@v3
name: Checkout the repository
- name: Set up conda
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
python-version: "3.10"
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: test
- name: Install Python dependencies
run: python3 -m pip install ruamel.yaml
- name: Install library dependencies with Conda (Windows)
# fmt needs to match the version of the windows-2022 runner selected to upload
# the cantera_shared.dll artifact
run: mamba install -q yaml-cpp mkl highfive fmt=8.1
shell: pwsh
if: matrix.os == 'windows-2022'
- name: Install Brew dependencies (macOS)
run: brew install --display-times hdf5
if: matrix.os == 'macos-11'
- name: Install Apt dependencies (Ubuntu)
run: sudo apt install libhdf5-dev libfmt-dev
if: matrix.os == 'ubuntu-22.04'
- name: Setup .NET Core SDK
uses: actions/setup-dotnet@v2
with:
dotnet-version: '6.x'
- name: Download the Cantera shared library (.so)
uses: actions/download-artifact@v3
with:
name: libcantera_shared-ubuntu-22.04.so
path: build/lib
- name: Download the Cantera shared library (.dylib)
uses: actions/download-artifact@v3
with:
name: libcantera_shared.dylib
path: build/lib
- name: Download the Cantera shared library (.dll)
uses: actions/download-artifact@v3
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