Nightly build (binaries) #1343
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| name: Nightly build (binaries) | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: "0 5 * * *" | |
| env: | |
| BUILD_TYPE: Release | |
| jobs: | |
| build: | |
| if: github.repository_owner == 'sbmlteam' | |
| name: | |
| ${{ matrix.platform }}, Parser option ${{ matrix.xml_parser_option }}, | |
| with namespaces ${{ matrix.with_namespace}}, strict includes ${{ | |
| matrix.strict }}, with examples ${{ matrix.with_examples}}, package option | |
| ${{ matrix.package_option}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [windows-latest, macos-latest, ubuntu-latest] | |
| xml_parser_option: ["-DWITH_EXPAT=ON"] | |
| with_namespace: ["True"] | |
| strict: ["True"] | |
| with_examples: ["True"] | |
| package_option: ["-DWITH_ALL_PACKAGES=ON", "-DWITH_STABLE_PACKAGES=ON"] | |
| language_bindings: | |
| [ | |
| "-DWITH_JAVA=True -DWITH_PYTHON=True -DWITH_R=OFF", | |
| ] | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: seanmiddleditch/gha-setup-ninja@master | |
| - name: Add msbuild to PATH (Windows) | |
| if: matrix.platform == 'windows-latest' | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| ### configure the operating system ### | |
| - name: Cache Windows dependencies and SWIG | |
| # On Windows, the dependencies live inside the source folder, ie `.`. | |
| # For the CI, we put SWIG there too, for simplicity. | |
| if: matrix.platform == 'windows-latest' | |
| id: cache-win-dependencies-static | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ./dependencies | |
| ./swig | |
| key: ${{ runner.os }}-dependencies-static-2 | |
| - name: Download pre-built Windows dependencies and SWIG | |
| # Windows dependencies have to be in a subfolder called `dependencies`, directly under the git repository root. | |
| # also gets SWIG, completing the set of dependencies needed for windows | |
| if: | |
| matrix.platform == 'windows-latest' && | |
| steps.cache-win-dependencies-static.outputs.cache-hit != 'true' | |
| shell: bash | |
| run: | | |
| curl -L https://github.com/sbmlteam/libSBML-dependencies/releases/download/latest/libSBML-dependencies-1.0.1-x64-Release-static.zip > dependencies.zip | |
| unzip dependencies.zip | |
| mv libSBML-dependencies-1.0.1-x64-Release-static dependencies | |
| curl -L https://prdownloads.sourceforge.net/swig/swigwin-3.0.12.zip > swig.zip | |
| unzip -o swig.zip -d swig | |
| - name: setup Windows environment | |
| # this is separate from the SWIG download itself, because it needs to be added to the path also when SWIG is cached | |
| if: matrix.platform == 'windows-latest' | |
| shell: bash | |
| run: | | |
| echo $GITHUB_WORKSPACE"/swig/swigwin-3.0.12/" >> $GITHUB_PATH | |
| echo RUNTIME_LINKING_OPTION="-DWITH_STATIC_RUNTIME=ON" >> "${GITHUB_ENV}" | |
| echo CSHARP_OPTION="-DWITH_CSHARP=True" >> "${GITHUB_ENV}" | |
| ./dev/utilities/expdef/expdef64.exe -dRlib.def -l R.dll | |
| echo R_PLATFORM_SPECIFIC_OPTIONS="-DR_LIB=${GITHUB_WORKSPACE}\Rlib.lib" >> "${GITHUB_ENV}" | |
| - name: Find Windows R include path | |
| # robust to R version changing | |
| if: matrix.platform == 'windows-latest' | |
| shell: bash | |
| run: | | |
| cd /c/Program\ Files/R/ | |
| R_INCLUDE_DIR_VERSION=$(ls -d *) | |
| echo R_INCLUDE_PATH="/c/Program Files/R/"$R_INCLUDE_DIR_VERSION"/include" >> "${GITHUB_ENV}" | |
| - name: Install Ubuntu dependencies | |
| # ubuntu already has SWIG but expat is too old | |
| if: matrix.platform == 'ubuntu-latest' | |
| shell: bash | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y check ccache | |
| echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}" | |
| echo CSHARP_OPTION="-DWITH_CSHARP=True" >> "${GITHUB_ENV}" | |
| git clone https://github.com/libexpat/libexpat | |
| cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat | |
| cmake --build libexpat | |
| cmake --install libexpat | |
| - name: Install MacOS dependencies | |
| # MacOS already has expat by default | |
| if: matrix.platform == 'macos-latest' | |
| shell: bash | |
| run: | | |
| brew install check swig ccache | |
| echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}" | |
| echo CSHARP_OPTION="-DWITH_CSHARP=OFF" >> "${GITHUB_ENV}" | |
| - name: Unix R options | |
| if: matrix.platform != 'windows-latest' | |
| shell: bash | |
| run: | |
| echo R_PLATFORM_SPECIFIC_OPTIONS="-DWITH_CREATE_R_SOURCE=ON | |
| -DWITH_SKIP_R_BINARY=ON" >> "${GITHUB_ENV}" | |
| ### setup ccache, not on Windows ### | |
| - name: Prepare ccache timestamp | |
| if: matrix.platform != 'windows-latest' | |
| id: ccache_cache_timestamp | |
| shell: cmake -P {0} | |
| run: | | |
| string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC) | |
| message("::set-output name=timestamp::${current_date}") | |
| - name: Set ccache cache directory | |
| if: matrix.platform != 'windows-latest' | |
| shell: bash | |
| run: | | |
| echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}" | |
| echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}" | |
| - name: cache ccache files | |
| if: matrix.platform != 'windows-latest' | |
| 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 }}- | |
| ### build the project ### | |
| - name: Create Build Environment | |
| run: cmake -E make_directory ${{runner.workspace}}/build | |
| - name: Configure CMake for XML_parser (expat) | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/build | |
| run: | | |
| mkdir ../install | |
| cmake $GITHUB_WORKSPACE \ | |
| -G "Ninja" \ | |
| -DCMAKE_INSTALL_PREFIX=../install \ | |
| -DCMAKE_BUILD_TYPE=$BUILD_TYPE \ | |
| -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_STANDARD=98 \ | |
| -DWITH_CHECK=True \ | |
| -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \ | |
| -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \ | |
| -DWITH_EXAMPLES=${{matrix.with_examples}} \ | |
| -DWITH_LIBXML=OFF \ | |
| ${{matrix.xml_parser_option}} \ | |
| ${{matrix.package_option}} \ | |
| ${{matrix.language_bindings}} \ | |
| ${R_PLATFORM_SPECIFIC_OPTIONS} \ | |
| -DR_INCLUDE_DIRS="$R_INCLUDE_PATH" \ | |
| ${RUNTIME_LINKING_OPTION} \ | |
| ${PYTHON_LINKING_OPTION} \ | |
| ${CSHARP_OPTION} | |
| - name: Build | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: | | |
| cmake --build . --config $BUILD_TYPE | |
| # - name: Build Unix R binaries from source package | |
| # if: matrix.platform != 'windows-latest' | |
| # shell: bash | |
| # working-directory: ${{runner.workspace}}/build | |
| # run: | | |
| # mkdir r-binaries | |
| # R CMD INSTALL -l r-binaries --build ./src/bindings/r/out/libSBML_5.19.3.tar.gz | |
| ### run tests ### | |
| - name: Test | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: ctest -C $BUILD_TYPE | |
| ### create binaries ### | |
| - name: Install | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: cmake --install . --config $BUILD_TYPE | |
| - name: Remove large .lib file on Windows | |
| ### file temporarily needed for bindings ### | |
| if: matrix.platform == 'windows-latest' | |
| working-directory: ${{runner.workspace}}/install | |
| shell: bash | |
| run: rm lib/libsbml-static.lib | |
| ### setup artifact environment ### | |
| - name: Store libSBML version in environment | |
| shell: bash | |
| run: echo "LIBSBML_VERSION=$( cat VERSION.txt)" >> "${GITHUB_ENV}" | |
| - name: Set artifact name suffix to stable packages | |
| if: matrix.package_option=='-DWITH_STABLE_PACKAGES=ON' | |
| shell: bash | |
| run: | | |
| echo "ARTIFACT_NAME_SUFFIX=stable-packages" >> "${GITHUB_ENV}" | |
| - name: Set artifact name suffix to all packages | |
| if: matrix.package_option=='-DWITH_ALL_PACKAGES=ON' | |
| shell: bash | |
| run: | | |
| echo "ARTIFACT_NAME_SUFFIX=all-packages" >> "${GITHUB_ENV}" | |
| ### Upload installed versions ### | |
| - name: Upload Windows binary archive | |
| if: matrix.platform == 'windows-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: | |
| Windows (zip, libSBML ${{env.LIBSBML_VERSION}}, | |
| ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }} | |
| path: ${{runner.workspace}}/install/* | |
| retention-days: 1 | |
| if-no-files-found: error | |
| - name: Upload MacOS binary archive | |
| if: matrix.platform == 'macos-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: | |
| MacOS (zip, libSBML ${{env.LIBSBML_VERSION}}, | |
| ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }} | |
| path: | | |
| ${{runner.workspace}}/install/* | |
| ${{runner.workspace}}/build/r-binaries/* | |
| retention-days: 1 | |
| if-no-files-found: error | |
| - name: Upload Ubuntu binary archive | |
| if: matrix.platform == 'ubuntu-latest' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: | |
| Ubuntu nightly (zip, libSBML ${{env.LIBSBML_VERSION}}, | |
| ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }} | |
| path: | | |
| ${{runner.workspace}}/install/* | |
| retention-days: 1 | |
| if-no-files-found: error | |
| manylinuxbuild: | |
| if: github.repository_owner == 'sbmlteam' | |
| name: | |
| ${{ matrix.container }}, Parser option ${{ matrix.xml_parser_option }}, | |
| with namespaces ${{ matrix.with_namespace}}, strict includes ${{ | |
| matrix.strict }}, with examples ${{ matrix.with_examples}}, package option | |
| ${{ matrix.package_option}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| platform: [ubuntu-latest] | |
| xml_parser_option: ["-DWITH_EXPAT=ON"] | |
| with_namespace: ["True"] | |
| strict: ["True"] | |
| with_examples: ["True"] | |
| package_option: ["-DWITH_ALL_PACKAGES=ON", "-DWITH_STABLE_PACKAGES=ON"] | |
| cpp_standard: [98] | |
| language_bindings: | |
| ["-DWITH_JAVA=True -DWITH_PYTHON=True"] | |
| container: ["quay.io/pypa/manylinux_2_28_x86_64"] | |
| runs-on: ${{ matrix.platform }} | |
| container: ${{ matrix.container}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: install Swig 4 from source | |
| run: | | |
| yum install -y pcre-devel | |
| echo "SWIG_DIR=/usr/local/swig/" >> "${GITHUB_ENV}" | |
| curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.0.2/swig-4.0.2.tar.gz/download > swig.tar.gz | |
| tar -zxvf swig.tar.gz | |
| cd swig-4.0.2/ | |
| ./configure --disable-dependency-tracking --prefix=$SWIG_DIR | |
| make clean | |
| make -j 2 | |
| make install | |
| swig -version | |
| - name: install CMake using pip | |
| run: | | |
| /opt/python/cp38-cp38/bin/pip install cmake | |
| ln -s /opt/python/cp38-cp38/bin/cmake /usr/bin/cmake | |
| ln -s /opt/python/cp38-cp38/bin/ctest /usr/bin/ctest | |
| cmake --version | |
| ctest --version | |
| - name: Install dependencies, configure, build | |
| run: | | |
| yum install -y libxml2-devel check-devel java-devel | |
| git clone https://github.com/libexpat/libexpat | |
| cmake -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat | |
| cmake --build libexpat | |
| cmake --install libexpat | |
| cd .. | |
| mkdir build | |
| cd build | |
| mkdir ../install | |
| cmake ../libsbml \ | |
| -DCMAKE_INSTALL_PREFIX=../install \ | |
| -DCMAKE_BUILD_TYPE=$BUILD_TYPE \ | |
| -DCMAKE_CXX_STANDARD=${{matrix.cpp_standard}} \ | |
| -DWITH_CHECK=True \ | |
| -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \ | |
| -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \ | |
| -DWITH_EXAMPLES=${{matrix.with_examples}} \ | |
| -DWITH_LIBXML=OFF \ | |
| ${{matrix.xml_parser_option}} \ | |
| ${{matrix.package_option}} \ | |
| ${{matrix.language_bindings}} \ | |
| -DPYTHON_EXECUTABLE=/opt/python/cp38-cp38/bin/python \ | |
| -DPYTHON_INCLUDE_DIR=/opt/python/cp38-cp38/include/python3.8/ \ | |
| -DWITH_STATIC_RUNTIME=ON \ | |
| -DPYTHON_USE_DYNAMIC_LOOKUP=ON | |
| cmake --build . --config $BUILD_TYPE | |
| - name: Test | |
| run: | | |
| cd ../build | |
| ctest -V -C $BUILD_TYPE | |
| ### create binaries ### | |
| - name: Install | |
| run: | | |
| cd ../build | |
| cmake --install . --config $BUILD_TYPE | |
| ### setup artifact environment ### | |
| - name: Store libSBML version in environment | |
| run: | | |
| echo "LIBSBML_VERSION=$( cat VERSION.txt)" >> "${GITHUB_ENV}" | |
| - name: Set artifact name suffix to stable packages | |
| if: matrix.package_option=='-DWITH_STABLE_PACKAGES=ON' | |
| run: | | |
| echo "ARTIFACT_NAME_SUFFIX=stable-packages" >> "${GITHUB_ENV}" | |
| - name: Set artifact name suffix to all packages | |
| if: matrix.package_option=='-DWITH_ALL_PACKAGES=ON' | |
| run: | | |
| echo "ARTIFACT_NAME_SUFFIX=all-packages" >> "${GITHUB_ENV}" | |
| - name: Upload Manylinux binary archive | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: | |
| Manylinux nightly (zip, libSBML ${{env.LIBSBML_VERSION}}, | |
| ${{env.ARTIFACT_NAME_SUFFIX}})-${{ strategy.job-index }} | |
| path: ../install |