Fix a bug and update the version to 0.2.2 #561
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| name: Build LibSBMLNetwork | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| pull_request: | |
| branches: | |
| - '**' | |
| jobs: | |
| build_on_OSs: | |
| name: Build RoadRunner on ${{ matrix.platform.name }}-python${{ matrix.python_version }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: | |
| - name: macos-12-release | |
| os_type: macos | |
| os_name: macos-12 | |
| build_type: Release | |
| build_python: ON | |
| - name: macos-12-debug | |
| os_type: macos | |
| os_name: macos-12 | |
| build_type: Debug | |
| build_python: ON | |
| - name: macos-latest-release | |
| os_type: macos | |
| os_name: macos-latest | |
| build_type: Release | |
| build_python: ON | |
| - name: macos-latest-debug | |
| os_type: macos | |
| os_name: macos-latest | |
| build_type: Debug | |
| build_python: ON | |
| - name: ubuntu-latest-release | |
| os_type: ubuntu | |
| os_name: ubuntu-latest | |
| build_type: Release | |
| build_python: ON | |
| - name: ubuntu-latest-debug | |
| os_type: ubuntu | |
| os_name: ubuntu-latest | |
| build_type: Debug | |
| build_python: ON | |
| - name: windows-latest-release | |
| os_type: windows | |
| os_name: windows-latest | |
| build_type: Release | |
| build_python: ON | |
| - name: windows-latest-debug | |
| os_type: windows | |
| os_name: windows-latest | |
| build_type: Debug | |
| build_python: OFF | |
| - name: manylinux_2_28-release | |
| os_type: manylinux | |
| os_name: ubuntu-latest | |
| container_image: quay.io/pypa/manylinux_2_28_x86_64 | |
| build_type: Release | |
| build_python: ON | |
| - name: manylinux_2_28-debug | |
| os_type: manylinux | |
| os_name: ubuntu-latest | |
| container_image: quay.io/pypa/manylinux_2_28_x86_64 | |
| build_type: Debug | |
| build_python: ON | |
| libroadrunner_deps_owner: [ "sys-bio" ] | |
| libroadrunner_deps_repo: [ "libroadrunner-deps" ] | |
| libroadrunner_deps_name: [ "libroadrunner-deps" ] | |
| libroadrunner_deps_release_version: [ "v2.1.2" ] | |
| python_version: [ "3.11" ] | |
| runs-on: ${{ matrix.platform.os_name }} | |
| container: | |
| image: ${{ matrix.platform.container_image || '' }} | |
| steps: | |
| - name: Checkout libSBMLNetwork | |
| uses: actions/checkout@v4 | |
| - name: Set MSVC as the default compiler on Windows | |
| if: matrix.platform.os_type == 'windows' | |
| uses: ilammy/msvc-dev-cmd@v1.6.0 | |
| - name: Upgrade gcc on Linux | |
| if: matrix.platform.os_type == 'manylinux' | |
| shell: bash | |
| run: | | |
| if [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then | |
| apt-get update | |
| apt-get install -y software-properties-common | |
| add-apt-repository -y ppa:ubuntu-toolchain-r/test | |
| apt-get update | |
| apt-get install -y gcc-11 g++-11 | |
| update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 90 | |
| update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 90 | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| dnf install -y gcc-toolset-11 | |
| scl enable gcc-toolset-11 bash | |
| echo "/opt/rh/gcc-toolset-11/root/usr/bin" >> "${GITHUB_PATH}" | |
| fi | |
| - name: Setup Ninja | |
| uses: seanmiddleditch/gha-setup-ninja@master | |
| - name: Get Host Architecture | |
| shell: bash | |
| run: | | |
| architecture=$(uname -m) | |
| echo "host_architecture=$architecture" >> "${GITHUB_ENV}" | |
| if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then | |
| echo "OSX_ARCHITECTURES=$architecture" >> "${GITHUB_ENV}" | |
| fi | |
| - name: Install ccache | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE} | |
| if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then | |
| brew install ccache | |
| elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then | |
| sudo apt-get update | |
| sudo apt-get install -y ccache | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| mkdir -p ccache | |
| cd ccache | |
| curl -L https://github.com/ccache/ccache/releases/download/v4.9.1/ccache-4.9.1.tar.gz > ccache.tar.gz | |
| tar -zxf ccache.tar.gz | |
| rm ccache.tar.gz | |
| mkdir -p build-ccache | |
| mkdir -p install-ccache | |
| cd build-ccache | |
| cmake -DCMAKE_INSTALL_PREFIX="$RUNNER_WORKSPACE/ccache/install-ccache" -DCMAKE_BUILD_TYPE=Release ../ccache-4.9.1 | |
| cmake --build . --target install | |
| echo "$RUNNER_WORKSPACE/ccache/install-ccache/bin" >> "${GITHUB_PATH}" | |
| fi | |
| - name: Prepare ccache timestamp on non-Windows platforms | |
| if: matrix.platform.os_type != 'windows' | |
| id: ccache_cache_timestamp | |
| shell: cmake -P {0} | |
| run: | | |
| string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC) | |
| message("::set-output name=timestamp::${current_date}") | |
| - name: Set ccache cache directory on non-Windows | |
| if: matrix.platform.os_type != 'windows' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE} | |
| echo "CCACHE_DIR=${RUNNER_WORKSPACE}/.ccache" >> "${GITHUB_ENV}" | |
| echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}" | |
| - name: Cache ccache files on non-Windows | |
| if: matrix.platform.os_type != 'windows' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${RUNNER_WORKSPACE}/.ccache | |
| key: | |
| ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp | |
| }} | |
| restore-keys: | | |
| ${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }} | |
| ${{ runner.os }}- | |
| - name: Setup Python for non-Manylinux platforms | |
| if: matrix.platform.build_python == 'ON' && matrix.platform.os_type != 'manylinux' | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python_version }} | |
| - name: Setup Python for Manylinux platforms | |
| if: matrix.platform.build_python == 'ON' && matrix.platform.os_type == 'manylinux' | |
| shell: bash | |
| run: | | |
| dnf install -y wget | |
| wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p /Miniconda3 | |
| /Miniconda3/bin/conda create -y --name python${{ matrix.python_version }} python=${{ matrix.python_version }} | |
| /Miniconda3/bin/conda init && bash ~/.bashrc && . ~/.bashrc cd ${RUNNER_WORKSPACE} | |
| echo "export PATH=/Miniconda3/envs/python${{ matrix.python_version }}/bin:$PATH" >> "${GITHUB_ENV}" | |
| - name: Download Dependencies binaries | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE} | |
| mkdir -p ${{ matrix.libroadrunner_deps_name }}-binaries | |
| cd ${{ matrix.libroadrunner_deps_name }}-binaries | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio") | |
| binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }} | |
| elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then | |
| os_version=$(sw_vers -productVersion | cut -d '.' -f 1) | |
| binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} | |
| elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then | |
| os_version=$(lsb_release -rs | cut -d '.' -f 1) | |
| binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }} | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| os_name="${{ matrix.platform.name }}" | |
| os_name_without_build_type="${os_name%%-*}" | |
| binary_file_name=${{ matrix.libroadrunner_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }} | |
| fi | |
| curl -LO "https://github.com/${{ matrix.libroadrunner_deps_owner }}/${{ matrix.libroadrunner_deps_repo }}/releases/download/${{ matrix.libroadrunner_deps_release_version }}/$binary_file_name.zip" | |
| unzip -q $binary_file_name.zip | |
| rm $binary_file_name.zip | |
| echo DEPENDENCIES_INSTALL_PREFIX="${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries" >> "${GITHUB_ENV}" | |
| - name: Create build directory | |
| shell: bash | |
| run: mkdir -p ${RUNNER_WORKSPACE}/build-libsbmlnetwork | |
| - name: Configure CMake for libBMLNetwork | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/build-libsbmlnetwork | |
| cmake $GITHUB_WORKSPACE \ | |
| -G "Ninja" \ | |
| -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_BUILD_TYPE=${{ matrix.platform.build_type }} \ | |
| -DCMAKE_OSX_ARCHITECTURES=${OSX_ARCHITECTURES} \ | |
| -DCMAKE_INSTALL_PREFIX="${RUNNER_WORKSPACE}/install-libsbmlnetwork" \ | |
| -DDEPENDENCIES_INSTALL_PREFIX=${DEPENDENCIES_INSTALL_PREFIX} \ | |
| -DWITH_PYTHON=${{ matrix.platform.build_python }} \ | |
| -DPYTHON_INSTALL_WITH_SETUP="ON" | |
| - name: Build and install libSBMLNetwork | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/build-libsbmlnetwork | |
| cmake --build . --target install --config ${{ matrix.platform.build_type }} | |
| - name: Install python packages | |
| if: matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE} | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| python -m pip install pytest ipython setuptools wheel | |
| python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork | |
| python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| python${{ matrix.python_version }} -m pip install --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org pytest ipython setuptools wheel | |
| python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork | |
| python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork | |
| else | |
| python${{ matrix.python_version }} -m pip install pytest ipython setuptools wheel | |
| python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork | |
| python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork | |
| fi | |
| - name: Run libSBMLNetwork tests | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork/tests | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| python -m pytest -p no:cacheprovider | |
| else | |
| python${{ matrix.python_version }} -m pytest -p no:cacheprovider | |
| fi | |
| - name: Set artifacts path and name | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE} | |
| artifacts_name="" | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio") | |
| echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-msvc$compiler_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}" | |
| elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then | |
| os_version=$(sw_vers -productVersion | cut -d '.' -f 1) | |
| echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-$os_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}" | |
| elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then | |
| os_version=$(lsb_release -rs | cut -d '.' -f 1) | |
| echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-$os_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}" | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| os_name="${{ matrix.platform.name }}" | |
| os_name_without_build_type="${os_name%%-*}" | |
| echo "artifacts_name=libsbmlnetwork-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}" | |
| fi | |
| echo "artifacts_path=../install-libsbmlnetwork" >> "${GITHUB_ENV}" | |
| - name: Upload libSBMLNetwork binaries | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: ${{env.artifacts_name}} | |
| path: ${{env.artifacts_path}} | |
| - name: Create libSBMLNetwork Python wheel artifacts | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| python setup.py bdist_wheel | |
| else | |
| python${{ matrix.python_version }} setup.py bdist_wheel | |
| fi | |
| - name: Rename libSBMLNetwork Python wheel artifacts | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork | |
| if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then | |
| mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/universal2/${host_architecture}/g") | |
| elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then | |
| mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/linux/manylinux_2_28/g") | |
| fi | |
| python_version_number=$(echo "${{ matrix.python_version }}" | tr -d '.') | |
| mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/cp${python_version_number}-cp${python_version_number}/py3-none/g") | |
| - name: Create SBMLNetwork Python wheel artifacts | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork | |
| if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then | |
| python setup.py bdist_wheel | |
| else | |
| python${{ matrix.python_version }} setup.py bdist_wheel | |
| fi | |
| - name: Set Python wheel artifacts path and name | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| shell: bash | |
| run: | | |
| cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages | |
| libsbmlnetwork_python_wheel_file_name=$(ls libsbmlnetwork/dist | grep '^libsbmlnetwork') | |
| echo "libsbmlnetwork_python_wheel_artifacts_name=${libsbmlnetwork_python_wheel_file_name}" >> "${GITHUB_ENV}" | |
| sbmlnetwork_python_wheel_file_name=$(ls sbmlnetwork/dist | grep '^sbmlnetwork') | |
| echo "sbmlnetwork_python_wheel_artifacts_name=${sbmlnetwork_python_wheel_file_name}" >> "${GITHUB_ENV}" | |
| # we need to use relative path as actions/upload-artifact@v1 cannot find it on containerized runners | |
| echo "libsbmlnetwork_python_wheel_artifacts_file=../install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork/dist/$libsbmlnetwork_python_wheel_file_name" >> "${GITHUB_ENV}" | |
| echo "sbmlnetwork_python_wheel_artifacts_file=../install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork/dist/$sbmlnetwork_python_wheel_file_name" >> "${GITHUB_ENV}" | |
| - name: Upload libSBMLNetwork Python wheel artifacts | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: ${{env.libsbmlnetwork_python_wheel_artifacts_name}} | |
| path: ${{env.libsbmlnetwork_python_wheel_artifacts_file}} | |
| - name: Upload SBMLNetwork Python wheel artifacts | |
| if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON' | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: ${{env.sbmlnetwork_python_wheel_artifacts_name}} | |
| path: ${{env.sbmlnetwork_python_wheel_artifacts_file}} |