Add basic converter for inferring reactions #454
Workflow file for this run
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| 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@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.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@v4 | |
| 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 |