Update GitHub Actions where needed #448
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CMake (Extensive build on PR to develepment) | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, ready_for_review, reopened] # defaults + ready_to_review | |
| branches: | |
| - development | |
| env: | |
| BUILD_TYPE: Release | |
| jobs: | |
| build: | |
| if: github.event.pull_request.draft == false # avoid triggering on draft | |
| 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: | |
| xml_parser_option: ["-DWITH_LIBXML"] | |
| platform: [windows-latest, macos-latest, ubuntu-latest] | |
| with_namespace: ["True", "False"] | |
| strict: ["True"] | |
| with_examples: ["True"] | |
| package_option: | |
| ["", "-DWITH_STABLE_PACKAGES=ON", "-DWITH_ALL_PACKAGES=ON"] | |
| language_bindings: | |
| ["-DWITH_JAVA=True -DWITH_CSHARP=True -DWITH_PYTHON=True -DWITH_R=OFF"] | |
| include: | |
| # to test the other two XML parsers while avoiding a combinatorial explosion in the number of jobs, | |
| # we additionally include just two runs / OS : one for Expat, and one for Xerces | |
| # extra Windows runs | |
| - xml_parser_option: "-DWITH_EXPAT" | |
| platform: windows-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| - xml_parser_option: "-DWITH_XERCES" | |
| platform: windows-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| # extra MacOS runs | |
| - xml_parser_option: "-DWITH_EXPAT" | |
| platform: macos-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| - xml_parser_option: "-DWITH_XERCES" | |
| platform: macos-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| # extra Ubuntu runs | |
| - xml_parser_option: "-DWITH_EXPAT" | |
| platform: ubuntu-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| - xml_parser_option: "-DWITH_XERCES" | |
| platform: ubuntu-latest | |
| with_namespace: "True" | |
| strict: "True" | |
| with_examples: "True" | |
| package_option: "-DWITH_ALL_PACKAGES=ON" | |
| language_bindings: "" | |
| runs-on: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: seanmiddleditch/gha-setup-ninja@master | |
| - name: Add msbuild to PATH (Windows) | |
| if: matrix.platform == 'windows-latest' | |
| uses: ilammy/[email protected] | |
| ### 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@v2 | |
| 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.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}" | |
| ./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" >> "${GITHUB_ENV}" | |
| - name: Install Ubuntu dependencies | |
| # ubuntu already has SWIG and libxml2 by default | |
| if: matrix.platform == 'ubuntu-latest' | |
| shell: bash | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y check libxerces-c-dev expat ccache | |
| echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${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 libxml2 by default | |
| if: matrix.platform == 'macos-latest' | |
| shell: bash | |
| run: | | |
| brew install check swig xerces-c expat ccache | |
| echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}" | |
| - name: Unix R options | |
| if: matrix.platform != 'windows-latest' | |
| shell: bash | |
| run: | |
| echo R_PLATFORM_SPECIFIC_OPTIONS="-DWITH_CREATE_R_SOURCE=ON | |
| -DWITH_SKIP_R_BINARY=ON" >> "${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@v2 | |
| with: | |
| path: ${{runner.workspace}}/.ccache | |
| key: | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ | |
| matrix.with_namespace }}-${{ matrix.strict }}-${{ | |
| steps.ccache_cache_timestamp.outputs.timestamp }} | |
| restore-keys: | | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }} | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}- | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}- | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}- | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}- | |
| ${{ runner.os }}-test-${{ matrix.xml_parser_option }}- | |
| ${{ runner.os }}-test- | |
| ${{ runner.os }}- | |
| ### build the project ### | |
| - name: Create Build Environment | |
| run: cmake -E make_directory ${{runner.workspace}}/build | |
| - name: Configure CMake for default XML_parser (LIBXML2) | |
| if: matrix.xml_parser_option == '-DWITH_LIBXML' # default option, no need to specify -DWITH_LIBXML=... | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/build | |
| run: | | |
| cmake $GITHUB_WORKSPACE \ | |
| -G "Ninja" \ | |
| -DCMAKE_BUILD_TYPE=$BUILD_TYPE \ | |
| -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_STANDARD=11 \ | |
| -DWITH_CHECK=True \ | |
| -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \ | |
| -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \ | |
| -DWITH_EXAMPLES=${{matrix.with_examples}} \ | |
| ${{matrix.package_option}} \ | |
| ${{matrix.language_bindings}} \ | |
| ${R_PLATFORM_SPECIFIC_OPTIONS} \ | |
| -DR_INCLUDE_DIRS="$R_INCLUDE_PATH" \ | |
| ${RUNTIME_LINKING_OPTION} \ | |
| ${PYTHON_LINKING_OPTION} | |
| - name: Configure CMake for non-default XML_parser | |
| if: matrix.xml_parser_option != '-DWITH_LIBXML' | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/build | |
| run: | | |
| cmake $GITHUB_WORKSPACE \ | |
| -DCMAKE_BUILD_TYPE=$BUILD_TYPE \ | |
| -DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \ | |
| -DCMAKE_CXX_STANDARD=11 \ | |
| -DWITH_CHECK=True \ | |
| -DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \ | |
| -DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \ | |
| -DWITH_EXAMPLES=${{matrix.with_examples}} \ | |
| -DWITH_LIBXML=False \ | |
| ${{matrix.xml_parser_option}}=True\ | |
| ${{matrix.package_option}} \ | |
| ${{matrix.language_bindings}} \ | |
| ${RUNTIME_LINKING_OPTION} \ | |
| ${PYTHON_LINKING_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' && matrix.xml_parser_option == '-DWITH_LIBXML' | |
| # 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 | |
| if: matrix.platform == 'macos-latest' | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: ctest -V -C $BUILD_TYPE -E test_cs | |
| - name: Test | |
| if: matrix.platform != 'macos-latest' | |
| working-directory: ${{runner.workspace}}/build | |
| shell: bash | |
| run: ctest -V -C $BUILD_TYPE |